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fff models simplex aligner  (Renfert GmbH)

 
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    Renfert GmbH fff models simplex aligner
    Fff Models Simplex Aligner, supplied by Renfert GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fff models simplex aligner/product/Renfert GmbH
    Average 90 stars, based on 1 article reviews
    fff models simplex aligner - by Bioz Stars, 2026-04
    90/100 stars

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    a Assessing Mendelian consistency of TR calls in an Ashkenazi trio using PacBio HiFi reads. The x -axis gives the LongTR score threshold to include calls, and the y -axis gives the percentage of TRs for which genotypes in the trio follow Mendelian consistency. Trio-TR pairs for which all members were called as homozygous for the reference allele were excluded. Dashed = TRGT; solid = LongTR. Note TRGT does not report a quality score and thus a single horizontal line is shown. Color indicates the size of the repeat unit (in bp) considered. b Concordance of TR genotypes obtained from PacBio HiFi with assembly alleles in <t>HG002.</t> TRs were binned by length of the repeat (in bp, bin size = 250bp) in GRCh38. The x -axis shows the TR length, and the y -axis shows the percent of alleles that match the assembly. Blue lines show when only length is considered. Orange lines show when both length and sequence are considered. Dashed = TRGT; solid = LongTR. The top panel shows the number of repeats in each bin, on a logarithmic scale
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    a Assessing Mendelian consistency of TR calls in an Ashkenazi trio using PacBio HiFi reads. The x -axis gives the LongTR score threshold to include calls, and the y -axis gives the percentage of TRs for which genotypes in the trio follow Mendelian consistency. Trio-TR pairs for which all members were called as homozygous for the reference allele were excluded. Dashed = TRGT; solid = LongTR. Note TRGT does not report a quality score and thus a single horizontal line is shown. Color indicates the size of the repeat unit (in bp) considered. b Concordance of TR genotypes obtained from PacBio HiFi with assembly alleles in <t>HG002.</t> TRs were binned by length of the repeat (in bp, bin size = 250bp) in GRCh38. The x -axis shows the TR length, and the y -axis shows the percent of alleles that match the assembly. Blue lines show when only length is considered. Orange lines show when both length and sequence are considered. Dashed = TRGT; solid = LongTR. The top panel shows the number of repeats in each bin, on a logarithmic scale
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    Image Search Results


    a Assessing Mendelian consistency of TR calls in an Ashkenazi trio using PacBio HiFi reads. The x -axis gives the LongTR score threshold to include calls, and the y -axis gives the percentage of TRs for which genotypes in the trio follow Mendelian consistency. Trio-TR pairs for which all members were called as homozygous for the reference allele were excluded. Dashed = TRGT; solid = LongTR. Note TRGT does not report a quality score and thus a single horizontal line is shown. Color indicates the size of the repeat unit (in bp) considered. b Concordance of TR genotypes obtained from PacBio HiFi with assembly alleles in HG002. TRs were binned by length of the repeat (in bp, bin size = 250bp) in GRCh38. The x -axis shows the TR length, and the y -axis shows the percent of alleles that match the assembly. Blue lines show when only length is considered. Orange lines show when both length and sequence are considered. Dashed = TRGT; solid = LongTR. The top panel shows the number of repeats in each bin, on a logarithmic scale

    Journal: Genome Biology

    Article Title: LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

    doi: 10.1186/s13059-024-03319-2

    Figure Lengend Snippet: a Assessing Mendelian consistency of TR calls in an Ashkenazi trio using PacBio HiFi reads. The x -axis gives the LongTR score threshold to include calls, and the y -axis gives the percentage of TRs for which genotypes in the trio follow Mendelian consistency. Trio-TR pairs for which all members were called as homozygous for the reference allele were excluded. Dashed = TRGT; solid = LongTR. Note TRGT does not report a quality score and thus a single horizontal line is shown. Color indicates the size of the repeat unit (in bp) considered. b Concordance of TR genotypes obtained from PacBio HiFi with assembly alleles in HG002. TRs were binned by length of the repeat (in bp, bin size = 250bp) in GRCh38. The x -axis shows the TR length, and the y -axis shows the percent of alleles that match the assembly. Blue lines show when only length is considered. Orange lines show when both length and sequence are considered. Dashed = TRGT; solid = LongTR. The top panel shows the number of repeats in each bin, on a logarithmic scale

    Article Snippet: HG002 assembly [ ]: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.0.1.fasta.gz adVNTR reference set of repeats [ ]: https://drive.google.com/file/d/1DetpBQySPNe2YAJa4FsjHn9qiRNS3wEV/view Oxford Nanopore Duplex data for HG002 [ ]: https://human-pangenomics.s3.amazonaws.com/index.html?prefix=submissions/0CB931D5-AE0C-4187-8BD8-B3A9C9BFDADE--UCSC_HG002_R1041_Duplex_Dorado/Dorado_v0.1.1/stereo_duplex/ Oxford Nanopore aligned and haplotagged Simplex SUP data for HG002 [ ]: https://42basepairs.com/download/s3/ont-open-data/giab_2023.05/analysis/variant_calling/hg002_sup_all/hg002.haplotagged.bam DeepVariant SNP calls used by WhatsHap [ ]: https://downloads.pacbcloud.com/public/revio/2022Q4/HG002-rep3/analysis/HG002.m84005_220827_014912_s1.GRCh38.deepvariant.phased.vcf.gz GIAB set of difficult to map regions [ ]: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_alllowmapandsegdupregions.bed.gz Illumina reads for HG002 [ ]: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/novoalign_bams/ .

    Techniques: Sequencing

    a Comparison of LongTR genotypes on ONT Duplex vs. PacBio HiFi data. For each call, we computed the average of the length of each allele relative to the GRCh38 reference. The x -axis gives the calls using PacBio data, and the y -axis gives the calls using ONT Duplex data. Bubble size scales with the number of calls at each coordinate. b IGV screenshot comparing PacBio HiFi reads vs. ONT Duplex reads at a TR genotyped by LongTR. The top window shows the assembly alignment, the middle window shows aligned HiFi reads, and the bottom window shows aligned ONT Duplex reads at a (AGTAAATAATG)n VNTR. All data is aligned to GRCh38. Red and blue denote PacBio HiFi reads from the two haplotypes of HG002 based on haplotag information. Gray reads have no haplotag information. HiFi reads were clipped at the large repeat insertion, resulting in an incorrect genotype call

    Journal: Genome Biology

    Article Title: LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

    doi: 10.1186/s13059-024-03319-2

    Figure Lengend Snippet: a Comparison of LongTR genotypes on ONT Duplex vs. PacBio HiFi data. For each call, we computed the average of the length of each allele relative to the GRCh38 reference. The x -axis gives the calls using PacBio data, and the y -axis gives the calls using ONT Duplex data. Bubble size scales with the number of calls at each coordinate. b IGV screenshot comparing PacBio HiFi reads vs. ONT Duplex reads at a TR genotyped by LongTR. The top window shows the assembly alignment, the middle window shows aligned HiFi reads, and the bottom window shows aligned ONT Duplex reads at a (AGTAAATAATG)n VNTR. All data is aligned to GRCh38. Red and blue denote PacBio HiFi reads from the two haplotypes of HG002 based on haplotag information. Gray reads have no haplotag information. HiFi reads were clipped at the large repeat insertion, resulting in an incorrect genotype call

    Article Snippet: HG002 assembly [ ]: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.0.1.fasta.gz adVNTR reference set of repeats [ ]: https://drive.google.com/file/d/1DetpBQySPNe2YAJa4FsjHn9qiRNS3wEV/view Oxford Nanopore Duplex data for HG002 [ ]: https://human-pangenomics.s3.amazonaws.com/index.html?prefix=submissions/0CB931D5-AE0C-4187-8BD8-B3A9C9BFDADE--UCSC_HG002_R1041_Duplex_Dorado/Dorado_v0.1.1/stereo_duplex/ Oxford Nanopore aligned and haplotagged Simplex SUP data for HG002 [ ]: https://42basepairs.com/download/s3/ont-open-data/giab_2023.05/analysis/variant_calling/hg002_sup_all/hg002.haplotagged.bam DeepVariant SNP calls used by WhatsHap [ ]: https://downloads.pacbcloud.com/public/revio/2022Q4/HG002-rep3/analysis/HG002.m84005_220827_014912_s1.GRCh38.deepvariant.phased.vcf.gz GIAB set of difficult to map regions [ ]: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_alllowmapandsegdupregions.bed.gz Illumina reads for HG002 [ ]: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/novoalign_bams/ .

    Techniques: Comparison