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Items: 1 to 20 of 79

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.

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.

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.

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.

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.

6.

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.

7.

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.

8.

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.

9.

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
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

Gao S, Sung WK, Nagarajan N.

J Comput Biol. 2011 Nov;18(11):1681-91. doi: 10.1089/cmb.2011.0170. Epub 2011 Sep 19.

20.

Dissect: detection and characterization of novel structural alterations in transcribed sequences.

Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC.

Bioinformatics. 2012 Jun 15;28(12):i179-87. doi: 10.1093/bioinformatics/bts214.

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