Journal: Genome Research

Article Title: ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

doi: 10.1101/gr.214346.116

Figure Lengend Snippet: De novo assembly results for Genome in a Bottle HG004 human genome short-read data with ABySS 1.0, ABySS 2.0, BCALM 2, DISCOVAR de novo, MEGAHIT, Minia, SOAPdenovo2, and SGA. To enable comparison with ABySS, the DISCOVAR de novo assembly was scaffolded with third-party scaffolders ABySS-Scaffold, LINKS , and BESST . For panels B – D , on the y -axes we show the range of NGA50 to NG50 to indicate uncertainty caused by real genomic variants between individual HG004 and the reference genome (GRCh38). On the x -axes, we show the number of breakpoints that occurred when aligning the sequences to the reference genome. ( A ) Peak memory usage and wall-clock time for the assemblers. ( B ) Contiguity and correctness metrics for contig sequences. ( C ) Contiguity and correctness metrics after scaffolding with mate-pair (MPET) reads. The SOAPdenovo2 result for this plot was excluded as an outlier with an NGA50 (NG50) value of 103 kbp (172 kbp) and 10,610 breakpoints. ( D ) Contiguity and correctness metrics after further scaffolding with BioNano optical mapping data, using BioNano's hybrid scaffolding pipeline.

Article Snippet: Interestingly, the t(1;16) translocation is seen in every assembly ( Supplemental Figs. S7–S12 ), and the t(6;8) translocation is also seen in the DISCOVAR de novo + BESST + BioNano assembly ( Supplemental Fig. S11 ).

Techniques: Comparison, Scaffolding

Journal: bioRxiv

Article Title: Rice Pan-genome Array (RPGA): an efficient genotyping solution for pan-genome-based accelerated crop improvement in rice

doi: 10.1101/2022.01.19.476884

Figure Lengend Snippet: The 12 LGs (linkage groups) correspond to 12 Sonasal chromosomes.

Article Snippet: To assess accuracy of RPGA-based Sonsal × PB 1121 ultra-high-density genetic map, the de novo whole genome assembly of one of the parental accession i.e., “Sonasal” was generated using Oxford Nanopore long-read sequencing.

Techniques:

Journal: Cells

Article Title: A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

doi: 10.3390/cells9081776

Figure Lengend Snippet: Schematic of the method used for genome assembly and for transposable element insertion (TEI) detection. Global variants (black) were detected from genome assemblies, and minor variants (gray) by remapping reads in these assemblies. The reference genomes used for RaGOO scaffolding were Dmel_R6.23 for G0 and for wild-type D. melanogaster strains, Dsim_R2.02 for wild-type D. simulans strains, and the G0 assembly for G73 and G0-F100.

Article Snippet: The previously described de novo D. melanogaster hybrid assembly obtained using BioNano and assembly merging [ ] reported a N50 of 9 Mb (L50 of 6 contigs) for the raw data, and a N50 of 21.3 Mb (L50 of 3 contigs) after merging.

Techniques: Scaffolding

Journal: Cells

Article Title: A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

doi: 10.3390/cells9081776

Figure Lengend Snippet: Estimation of the TE percentage in the D. melanogaster and D. simulans genomes (isogenic wild-type strains). ( a ) Estimation of the TE percentage using RepeatMasker (ONT chromosome assemblies), and dnaPipeTE or TEcount (Illumina reads). ( b ) Correlations between the estimates obtained with the indicated methods.

Article Snippet: The previously described de novo D. melanogaster hybrid assembly obtained using BioNano and assembly merging [ ] reported a N50 of 9 Mb (L50 of 6 contigs) for the raw data, and a N50 of 21.3 Mb (L50 of 3 contigs) after merging.

Techniques:

Journal: Cells

Article Title: A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

doi: 10.3390/cells9081776

Figure Lengend Snippet: Global variant copy numbers in wild-type D melanogaster and D. simulans strains. ( a ) Number of shared global variants among strains. The color scale (on the right of each panel) shows the distance based on the number of pairwise shared insertions (indicated in black in the figure). Values in white correspond to the total numbers of the identified insertions for the considered strains. ( b ) Mean TEI numbers for the indicated TE groups computed in the wild-type D melanogaster and D. simulans strains based on the ONT chromosome assemblies.

Article Snippet: The previously described de novo D. melanogaster hybrid assembly obtained using BioNano and assembly merging [ ] reported a N50 of 9 Mb (L50 of 6 contigs) for the raw data, and a N50 of 21.3 Mb (L50 of 3 contigs) after merging.

Techniques: Variant Assay

Journal: Cells

Article Title: A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

doi: 10.3390/cells9081776

Figure Lengend Snippet: Global variant sequence analysis in wild-type D. melanogaster and D. simulans strains. ( a ) Distributions of TE copy lengths (i.e., fragment size) in bp for all global variants across strains and TE groups. ( b ) Intra-family sequence divergence (average Kimura distance) computed per strain and per TE family.

Article Snippet: The previously described de novo D. melanogaster hybrid assembly obtained using BioNano and assembly merging [ ] reported a N50 of 9 Mb (L50 of 6 contigs) for the raw data, and a N50 of 21.3 Mb (L50 of 3 contigs) after merging.

Techniques: Variant Assay, Sequencing

Journal: Cells

Article Title: A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

doi: 10.3390/cells9081776

Figure Lengend Snippet: piRNA analyses in wild-type D. melanogaster and D. simulans strains. ( a ) Normalized piRNA counts (log10) relative to genome occupancy for all strains and the two species and linear regression curve. Each dot is a TE family. ( b ) Results for the dmgoth63 and dsgoth31 strains are shown as examples. Uniquely mapping piRNAs along ONT chromosome assemblies (black, normalized piRNA counts). Global variants identified along ONT chromosome assemblies (gray). Red arrows indicate flamenco (X chromosome) and 42AB (2R chromosome). Data for the other strains are provided in . The off-scale peaks might correspond to microRNAs that are absent from miRBase.

Article Snippet: The previously described de novo D. melanogaster hybrid assembly obtained using BioNano and assembly merging [ ] reported a N50 of 9 Mb (L50 of 6 contigs) for the raw data, and a N50 of 21.3 Mb (L50 of 3 contigs) after merging.

Techniques:

Journal: bioRxiv

Article Title: Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outcrossed mapping populations

doi: 10.1101/119271

Figure Lengend Snippet: (a) the estimated RFs along the scaffold based on 30 independent runs. Each gray line plot represents a independent run. x - and y -axis represent the SNP positions (Kb) on the scaffold 15 and the estimated RFs between the adjoining SNPs, respectively. Solid dots indicate the mean RFs at that position. There is a misassembly around 177Kb, where the estimated RFs are 0.321 ± 0.117. (b) and (c), the first ~ 166kb of scaffold 15 is collinear with NSP306v2 scaffold 4, while the last ~138kb is collinear with NSP306v2 scaffold 40002.

Article Snippet: Misassembly identified by BioNano maps in NSP306v2 de novo genome assembly.

Techniques:

Journal: bioRxiv

Article Title: Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outcrossed mapping populations

doi: 10.1101/119271

Figure Lengend Snippet: (a) dot plots for the physical distance against the estimated RFs for ITR_r1.0 scaffold pairs that mapped to the same NSP306v2 scaffolds. (b) the discrepancies between NSP306v2 and ITR_r1.0 were removed. We added a density plot (range from green to red) as well as a smoothed conditional mean plot (blue) calculated using generalized additive model (GAM). (c) dot plots for the physical distance against the estimated RFs for scaffold pairs that come from the same pseudomolecule. (d) histograms of the estimated RFs for scaffold pairs that come from different pseudomolecules.

Article Snippet: Misassembly identified by BioNano maps in NSP306v2 de novo genome assembly.

Techniques:

Journal: bioRxiv

Article Title: Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outcrossed mapping populations

doi: 10.1101/119271

Figure Lengend Snippet: (a)-(c) depict the syntenic map for three linkage groups. The scaffolds are represented by gray blocks. NSP306v2 scaffolds are placed at the top, while the ITR_r1.0 scaffolds are at the bottom. NSP306v2 scaffolds labeled with ‘(−)’ are placed in reverse direction. The apparent ‘banding’ pattern in the bottom scaffolds is just due to the fact that many of the ITR_r1.0 scaffolds are too small to distinguish by eye. A quadrilateral is used to depict the mapping information between an upper and a bottom scaffold. The blocks that represent NSP306v2 scaffold 1 are shaded with slashes.

Article Snippet: Misassembly identified by BioNano maps in NSP306v2 de novo genome assembly.

Techniques: Labeling