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Results: 1 to 20 of 93

1.

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation.

Naeem R, Rashid M, Pain A.

Bioinformatics. 2013 Feb 1;29(3):391-2. doi: 10.1093/bioinformatics/bts684. Epub 2012 Nov 28.

PMID:
23193222
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Rapid identification of non-human sequences in high-throughput sequencing datasets.

Bhaduri A, Qu K, Lee CS, Ungewickell A, Khavari PA.

Bioinformatics. 2012 Apr 15;28(8):1174-5. doi: 10.1093/bioinformatics/bts100. Epub 2012 Feb 28.

PMID:
22377895
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma.

Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA.

Genome Res. 2012 Feb;22(2):299-306. doi: 10.1101/gr.126516.111. Epub 2011 Oct 18.

PMID:
22009989
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.

Boisvert S, Laviolette F, Corbeil J.

J Comput Biol. 2010 Nov;17(11):1519-33. doi: 10.1089/cmb.2009.0238. Epub 2010 Oct 20.

PMID:
20958248
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A.

BMC Bioinformatics. 2011;12 Suppl 6:S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.

PMID:
21989211
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.

Jiang H, An L, Lin SM, Feng G, Qiu Y.

PLoS One. 2012;7(10):e46450. doi: 10.1371/journal.pone.0046450. Epub 2012 Oct 1. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/c08da7e7-60fe-4f7d-a457-299bf9f24148.

PMID:
23049702
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Identifying viral integration sites using SeqMap 2.0.

Hawkins TB, Dantzer J, Peters B, Dinauer M, Mockaitis K, Mooney S, Cornetta K.

Bioinformatics. 2011 Mar 1;27(5):720-2. doi: 10.1093/bioinformatics/btq722. Epub 2011 Jan 17.

PMID:
21245052
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

PathSeq: software to identify or discover microbes by deep sequencing of human tissue.

Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M.

Nat Biotechnol. 2011 May;29(5):393-6. doi: 10.1038/nbt.1868. No abstract available.

PMID:
21552235
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.

Prosperi MC, Salemi M.

Bioinformatics. 2012 Jan 1;28(1):132-3. doi: 10.1093/bioinformatics/btr627. Epub 2011 Nov 15.

PMID:
22088846
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species.

Wang Y, Leung HC, Yiu SM, Chin FY.

J Comput Biol. 2012 Feb;19(2):241-9. doi: 10.1089/cmb.2011.0276.

PMID:
22300323
[PubMed - indexed for MEDLINE]
11.

Enrich: software for analysis of protein function by enrichment and depletion of variants.

Fowler DM, Araya CL, Gerard W, Fields S.

Bioinformatics. 2011 Dec 15;27(24):3430-1. doi: 10.1093/bioinformatics/btr577. Epub 2011 Oct 17.

PMID:
22006916
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Das S, Vikalo H.

Bioinformatics. 2012 Jul 1;28(13):1677-83. doi: 10.1093/bioinformatics/bts256. Epub 2012 May 7.

PMID:
22569177
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.

Kong Y.

Genomics. 2011 Aug;98(2):152-3. doi: 10.1016/j.ygeno.2011.05.009. Epub 2011 May 30.

PMID:
21651976
[PubMed - indexed for MEDLINE]
Free Article
14.

Accurate estimation of short read mapping quality for next-generation genome sequencing.

Ruffalo M, Koyutürk M, Ray S, LaFramboise T.

Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.

PMID:
22962451
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Informed and automated k-mer size selection for genome assembly.

Chikhi R, Medvedev P.

Bioinformatics. 2014 Jan 1;30(1):31-7. doi: 10.1093/bioinformatics/btt310. Epub 2013 Jun 3.

PMID:
23732276
[PubMed - indexed for MEDLINE]
16.

Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyutürk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

PMID:
21856737
[PubMed - indexed for MEDLINE]
Free Article
17.

GapFiller: a de novo assembly approach to fill the gap within paired reads.

Nadalin F, Vezzi F, Policriti A.

BMC Bioinformatics. 2012;13 Suppl 14:S8. doi: 10.1186/1471-2105-13-S14-S8. Epub 2012 Sep 7.

PMID:
23095524
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Long read alignment based on maximal exact match seeds.

Liu Y, Schmidt B.

Bioinformatics. 2012 Sep 15;28(18):i318-i324. doi: 10.1093/bioinformatics/bts414.

PMID:
22962447
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence.

Blanca JM, Pascual L, Ziarsolo P, Nuez F, Cañizares J.

BMC Genomics. 2011 Jun 2;12:285. doi: 10.1186/1471-2164-12-285.

PMID:
21635747
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

ReadDB provides efficient storage for mapped short reads.

Rolfe PA, Gifford DK.

BMC Bioinformatics. 2011 Jul 7;12:278. doi: 10.1186/1471-2105-12-278.

PMID:
21736741
[PubMed - indexed for MEDLINE]
Free PMC Article

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