publication . Article . Other literature type . 2017

ARCS: scaffolding genome drafts with linked reads

Yeo, Sarah; Coombe, Lauren; Warren, René L; Chu, Justin; Birol, Inanç;
Open Access
  • Published: 01 Oct 2017 Journal: Bioinformatics, volume 34, pages 725-731 (issn: 1367-4803, eissn: 1460-2059, Copyright policy)
  • Publisher: Oxford University Press (OUP)
Abstract
Abstract Motivation Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA—a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10 × Genomics. Results Here, we present ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiens genome assembly can be increased over six-fold, u...
Subjects
free text keywords: Shotgun, Bioinformatics, Genome, Human genome, Computer science, Original Papers, Genome Analysis
Funded by
NIH| De Novo Assembly Tools: Research with Unbiased Engines (DNA-TRUE)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG007182-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
17 references, page 1 of 2

Adey A.et al (2014) In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res., 24, 2041–2049.25327137 [OpenAIRE] [PubMed]

Altschul S.F.et al (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–410.2231712 [OpenAIRE] [PubMed]

Goodwin S.et al (2016) Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet., 17, 333–351.27184599 [PubMed]

Hunt M.et al (2014) A comprehensive evaluation of assembly scaffolding tools. Genome Biol., 15, R42.24581555 [OpenAIRE] [PubMed]

Jackman S.D.et al (2017) ABySS 2.0: resource-efficient assembly of large genomes using a bloom filter. Genome Res., doi: 10.1101/gr.214346.116.

Kuleshov V.et al (2014) Whole-genome haplotyping using long reads and statistical methods. Nat. Biotechnol., 32, 261–266.24561555 [OpenAIRE] [PubMed]

Kuleshov V.et al (2016) Genome assembly from synthetic long read clouds. Bioinformatics, 32, i216–i224.27307620 [OpenAIRE] [PubMed]

Krzywinski M.et al (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639–1645.19541911 [OpenAIRE] [PubMed]

Li H. (2015) BFC: correcting Illumina sequencing errors. Bioinformatics, 31, 2885–2887.25953801 [OpenAIRE] [PubMed]

Li H., Durbin R. (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics, 26, 589–595.20080505 [OpenAIRE] [PubMed]

Mostovoy Y.et al (2016) A hybrid approach for de novo human genome sequence assembly and phasing. Nat. Methods, 13, 587–590.27159086 [OpenAIRE] [PubMed]

Narasimhan V.M.et al (2016) Health and population effects of rare gene knockouts in adult humans with related parents. Science, 352, 474–477.26940866 [OpenAIRE] [PubMed]

O’connell J.et al (2015) NxTrim: optimized trimming of Illumina mate pair reads. Bioinformatics, 31, 2035–2037.25661542 [PubMed]

Warren R.L.et al (2015) LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience, 4, 35.26244089 [OpenAIRE] [PubMed]

Weisenfeld N.I.et al (2017) Direct determination of diploid genome sequences. Genome Res, 27, 757–767.

17 references, page 1 of 2
Abstract
Abstract Motivation Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA—a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10 × Genomics. Results Here, we present ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiens genome assembly can be increased over six-fold, u...
Subjects
free text keywords: Shotgun, Bioinformatics, Genome, Human genome, Computer science, Original Papers, Genome Analysis
Funded by
NIH| De Novo Assembly Tools: Research with Unbiased Engines (DNA-TRUE)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG007182-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
17 references, page 1 of 2

Adey A.et al (2014) In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res., 24, 2041–2049.25327137 [OpenAIRE] [PubMed]

Altschul S.F.et al (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–410.2231712 [OpenAIRE] [PubMed]

Goodwin S.et al (2016) Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet., 17, 333–351.27184599 [PubMed]

Hunt M.et al (2014) A comprehensive evaluation of assembly scaffolding tools. Genome Biol., 15, R42.24581555 [OpenAIRE] [PubMed]

Jackman S.D.et al (2017) ABySS 2.0: resource-efficient assembly of large genomes using a bloom filter. Genome Res., doi: 10.1101/gr.214346.116.

Kuleshov V.et al (2014) Whole-genome haplotyping using long reads and statistical methods. Nat. Biotechnol., 32, 261–266.24561555 [OpenAIRE] [PubMed]

Kuleshov V.et al (2016) Genome assembly from synthetic long read clouds. Bioinformatics, 32, i216–i224.27307620 [OpenAIRE] [PubMed]

Krzywinski M.et al (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639–1645.19541911 [OpenAIRE] [PubMed]

Li H. (2015) BFC: correcting Illumina sequencing errors. Bioinformatics, 31, 2885–2887.25953801 [OpenAIRE] [PubMed]

Li H., Durbin R. (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics, 26, 589–595.20080505 [OpenAIRE] [PubMed]

Mostovoy Y.et al (2016) A hybrid approach for de novo human genome sequence assembly and phasing. Nat. Methods, 13, 587–590.27159086 [OpenAIRE] [PubMed]

Narasimhan V.M.et al (2016) Health and population effects of rare gene knockouts in adult humans with related parents. Science, 352, 474–477.26940866 [OpenAIRE] [PubMed]

O’connell J.et al (2015) NxTrim: optimized trimming of Illumina mate pair reads. Bioinformatics, 31, 2035–2037.25661542 [PubMed]

Warren R.L.et al (2015) LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience, 4, 35.26244089 [OpenAIRE] [PubMed]

Weisenfeld N.I.et al (2017) Direct determination of diploid genome sequences. Genome Res, 27, 757–767.

17 references, page 1 of 2
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publication . Article . Other literature type . 2017

ARCS: scaffolding genome drafts with linked reads

Yeo, Sarah; Coombe, Lauren; Warren, René L; Chu, Justin; Birol, Inanç;