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MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. Treangen TJ, et al. Genome Biol. 2013 Jan 15;14(1):R2. doi: 10.1186/gb-2013-14-1-r2. Genome Biol. 2013. PMID: 23320958 Free PMC article.
Mash: fast genome and metagenome distance estimation using MinHash.
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Ondov BD, et al. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x. Genome Biol. 2016. PMID: 27323842 Free PMC article.
An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.
Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH. Ondov BD, et al. Bioinformatics. 2010 Aug 1;26(15):1901-2. doi: 10.1093/bioinformatics/btq291. Epub 2010 Jun 18. Bioinformatics. 2010. PMID: 20562417 Free PMC article.
Mash Screen: high-throughput sequence containment estimation for genome discovery.
Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. Ondov BD, et al. Genome Biol. 2019 Nov 5;20(1):232. doi: 10.1186/s13059-019-1841-x. Genome Biol. 2019. PMID: 31690338 Free PMC article.
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.
Ondov BD, Varadarajan A, Passalacqua KD, Bergman NH. Ondov BD, et al. Bioinformatics. 2008 Dec 1;24(23):2776-7. doi: 10.1093/bioinformatics/btn512. Epub 2008 Oct 7. Bioinformatics. 2008. PMID: 18842598 Free PMC article.
Interactive metagenomic visualization in a Web browser.
Ondov BD, Bergman NH, Phillippy AM. Ondov BD, et al. BMC Bioinformatics. 2011 Sep 30;12:385. doi: 10.1186/1471-2105-12-385. BMC Bioinformatics. 2011. PMID: 21961884 Free PMC article.
Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis.
Harrington R, Ondov BD, Radune D, Friss MB, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D, Friedlander AM, Burans JP, Rosovitz MJ, Treangen T, Phillippy AM, Bergman NH. Harrington R, et al. Among authors: ondov bd. Genome Announc. 2013 Jan;1(1):e00067-12. doi: 10.1128/genomeA.00067-12. Epub 2013 Jan 15. Genome Announc. 2013. PMID: 23405332 Free PMC article.
Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923.
Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ. Treangen TJ, et al. Genome Announc. 2014 Nov 6;2(6):e01110-14. doi: 10.1128/genomeA.01110-14. Genome Announc. 2014. PMID: 25377701 Free PMC article.
BLAST-based validation of metagenomic sequence assignments.
Bazinet AL, Ondov BD, Sommer DD, Ratnayake S. Bazinet AL, et al. Among authors: ondov bd. PeerJ. 2018 May 28;6:e4892. doi: 10.7717/peerj.4892. eCollection 2018. PeerJ. 2018. PMID: 29868286 Free PMC article.
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