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Bluepippintm Dye Free, supplied by Sage Science, used in various techniques. Bioz Stars score: 96/100, based on 3509 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bluepippintm+dye+free/BluePippin/pm38917803-807-172-179
Average 96 stars, based on 3509 article reviews
Bluepippintm Dye Free, supplied by Sage Science, used in various techniques. Bioz Stars score: 96/100, based on 3509 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bluepippintm+dye+free/BluePippin/pm38917803-807-172-179
Average 96 stars, based on 3509 article reviews
bluepippintm dye free - by Bioz Stars,
2026-09
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Recombinant:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Modification:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – DNA Purification:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – dsDNA Assay:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – DNA Ligation:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Ligation:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Sequencing:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Formalin-fixed Paraffin-Embedded:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Agarose Gel Electrophoresis:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Binding Assay:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Imaging:Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – Resource ll OPEN ACCESS Article Title: Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NA12878 (SRR622457) Auton et al.88 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ SRR622/SRR622457 PCAWG short-read sequencing datasets Campbell et al.3 https://dcc.icgc.org/pcawg Anotations for PCAWG datasets Campbell et al.3 https://dcc.icgc.org/releases/PCAWG ICGC sequencing datasets Hudson et al.44 https://dcc.icgc.org/ dbSNP (build 151) Sherry et al.89 ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ human_9606_b151_GRCh38p7/VCF/ common_all_20180418.vcf.gz GRCh38 reference genome UCSC Genome Browser https://hgdownload.soe.ucsc.edu/ downloads.html CHM13 reference genome Nurk et al.90 https://github.com/marbl/CHM13 Experimental models: Cell lines U2OS cells American Type Culture Collection (ATCC) Cat# HTB-96TM; RRID:CVCL_0042 NCI-BL1184 cells American Type Culture Collection (ATCC) Cat# CRL-5949TM; RRID:CVCL_2635 NCI-H1184 cells American Type Culture Collection (ATCC) Cat# CRL-5858TM; RRID:CVCL_1458 Hs-746T cells American Type Culture Collection (ATCC) Cat# HTB-135; RRID:CVCL_0333 Software and algorithms TelFuse This paper https://github.com/ktan8/teltools/ TelSize This paper https://github.com/ktan8/teltools/ Minimap2 v2.17-r941 Li91 https://github.com/lh3/minimap2 BWA-MEM v0.7.17-r1188 Li92 https://github.com/lh3/bwa SAMtools v1.10 Li et al.93 https://github.com/samtools/samtools R v4.2.0 R Foundation for Statistical Computing94 https://www.r-project.org/ Python v3.7.4 Van Rossum et al.95 https://www.python.org/ Perl v5.26.2 Wall et al.96 http://www.perl.org/ Integrative Genomics Viewer (IGV) Thorvaldsdóttir et al.97 https://software.broadinstitute.org/ software/igv/ Bonito v0.3.5 Oxford Nanopore Technologies (ONT) https://github.com/nanoporetech/bonito Bonito basecalling model for telomeric reads Tan et al.98 https://github.com/ktan8/ nanopore_telomere_basecall Other Covaris g-TUBE Covaris Cat# 520079 Megaruptor 3 system Diagenode B06010003 PippinHT Sage Science Cat# HTP0001 Sequel IIe instrument Pacific Biosciences (PacBio) – |