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Items: 18

1.

Tigmint: correcting assembly errors using linked reads from large molecules.

Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, Birol I.

BMC Bioinformatics. 2018 Oct 26;19(1):393. doi: 10.1186/s12859-018-2425-6.

2.

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL.

BMC Bioinformatics. 2018 Jun 20;19(1):234. doi: 10.1186/s12859-018-2243-x.

3.

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Khan H, Mohamadi H, Vandervalk BP, Warren RL, Chu J, Birol I.

Bioinformatics. 2018 May 15;34(10):1697-1704. doi: 10.1093/bioinformatics/btx839.

4.

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.

Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H, Gibb EA, Pandoh P, Kirk H, Zhao Y, Jones M, Mungall AJ, Coope R, Pleasance S, Moore RA, Holt RA, Round JM, Ohora S, Walle BV, Veldhoen N, Helbing CC, Birol I.

Nat Commun. 2017 Nov 10;8(1):1433. doi: 10.1038/s41467-017-01316-7.

5.

Kollector: transcript-informed, targeted de novo assembly of gene loci.

Kucuk E, Chu J, Vandervalk BP, Austin Hammond S, Warren RL.

Bioinformatics. 2017 Sep 1;33(17):2789. doi: 10.1093/bioinformatics/btx405. No abstract available.

6.

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

Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I.

Genome Res. 2017 May;27(5):768-777. doi: 10.1101/gr.214346.116. Epub 2017 Feb 23.

7.

Kollector: transcript-informed, targeted de novo assembly of gene loci.

Kucuk E, Chu J, Vandervalk BP, Hammond SA, Warren RL, Birol I.

Bioinformatics. 2017 Jun 15;33(12):1782-1788. doi: 10.1093/bioinformatics/btx078. Erratum in: Bioinformatics. 2017 Sep 1;33(17 ):2789.

8.

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

Coombe L, Warren RL, Jackman SD, Yang C, Vandervalk BP, Moore RA, Pleasance S, Coope RJ, Bohlmann J, Holt RA, Jones SJ, Birol I.

PLoS One. 2016 Sep 15;11(9):e0163059. doi: 10.1371/journal.pone.0163059. eCollection 2016.

9.

ntHash: recursive nucleotide hashing.

Mohamadi H, Chu J, Vandervalk BP, Birol I.

Bioinformatics. 2016 Nov 15;32(22):3492-3494. Epub 2016 Jul 16.

10.

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJ, Bohlmann J, Birol I.

Genome Biol Evol. 2015 Dec 8;8(1):29-41. doi: 10.1093/gbe/evv244.

11.

Spaced Seed Data Structures for De Novo Assembly.

Birol I, Chu J, Mohamadi H, Jackman SD, Raghavan K, Vandervalk BP, Raymond A, Warren RL.

Int J Genomics. 2015;2015:196591. doi: 10.1155/2015/196591. Epub 2015 Oct 11.

12.

Konnector v2.0: pseudo-long reads from paired-end sequencing data.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.

BMC Med Genomics. 2015;8 Suppl 3:S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23.

13.

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.

Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJ, Birol I.

Gigascience. 2015 Aug 4;4:35. doi: 10.1186/s13742-015-0076-3. eCollection 2015.

14.

Sealer: a scalable gap-closing application for finishing draft genomes.

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.

BMC Bioinformatics. 2015 Jul 25;16:230. doi: 10.1186/s12859-015-0663-4.

15.

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

Warren RL, Keeling CI, Yuen MM, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJ, MacKay J, Birol I, Bohlmann J.

Plant J. 2015 Jul;83(2):189-212. doi: 10.1111/tpj.12886. Epub 2015 Jun 19.

16.

DIDA: Distributed Indexing Dispatched Alignment.

Mohamadi H, Vandervalk BP, Raymond A, Jackman SD, Chu J, Breshears CP, Birol I.

PLoS One. 2015 Apr 29;10(4):e0126409. doi: 10.1371/journal.pone.0126409. eCollection 2015.

17.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.

Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B, Yanchuk A, Ritland C, Boyle B, Bousquet J, Ritland K, Mackay J, Bohlmann J, Jones SJ.

Bioinformatics. 2013 Jun 15;29(12):1492-7. doi: 10.1093/bioinformatics/btt178. Epub 2013 May 22.

18.

Moby and Moby 2: creatures of the deep (web).

Vandervalk BP, McCarthy EL, Wilkinson MD.

Brief Bioinform. 2009 Mar;10(2):114-28. doi: 10.1093/bib/bbn051. Epub 2009 Jan 16.

PMID:
19151099

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