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242 results
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Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL. Wood DE, et al. Among authors: salzberg sl. Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46. Genome Biol. 2014. PMID: 24580807 Free PMC article.
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL. Langmead B, et al. Among authors: salzberg sl. Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4. Genome Biol. 2009. PMID: 19261174 Free PMC article.
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.
Brady A, Salzberg SL. Brady A, et al. Among authors: salzberg sl. Nat Methods. 2009 Sep;6(9):673-6. doi: 10.1038/nmeth.1358. Epub 2009 Aug 2. Nat Methods. 2009. PMID: 19648916 Free PMC article.
Quake: quality-aware detection and correction of sequencing errors.
Kelley DR, Schatz MC, Salzberg SL. Kelley DR, et al. Among authors: salzberg sl. Genome Biol. 2010;11(11):R116. doi: 10.1186/gb-2010-11-11-r116. Epub 2010 Nov 29. Genome Biol. 2010. PMID: 21114842 Free PMC article.
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.
Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL. Kelley DR, et al. Among authors: salzberg sl. Nucleic Acids Res. 2012 Jan;40(1):e9. doi: 10.1093/nar/gkr1067. Epub 2011 Nov 18. Nucleic Acids Res. 2012. PMID: 22102569 Free PMC article.
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. Kim D, et al. Among authors: salzberg sl. Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36. Genome Biol. 2013. PMID: 23618408 Free PMC article.
Centrifuge: rapid and sensitive classification of metagenomic sequences.
Kim D, Song L, Breitwieser FP, Salzberg SL. Kim D, et al. Among authors: salzberg sl. Genome Res. 2016 Dec;26(12):1721-1729. doi: 10.1101/gr.210641.116. Epub 2016 Oct 17. Genome Res. 2016. PMID: 27852649 Free PMC article.
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.
Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL. Zimin AV, et al. Among authors: salzberg sl. Genome Res. 2017 May;27(5):787-792. doi: 10.1101/gr.213405.116. Epub 2017 Jan 27. Genome Res. 2017. PMID: 28130360 Free PMC article.
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.
Breitwieser FP, Baker DN, Salzberg SL. Breitwieser FP, et al. Among authors: salzberg sl. Genome Biol. 2018 Nov 16;19(1):198. doi: 10.1186/s13059-018-1568-0. Genome Biol. 2018. PMID: 30445993 Free PMC article.
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.
Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL. Pertea M, et al. Among authors: salzberg sl. Genome Biol. 2018 Nov 28;19(1):208. doi: 10.1186/s13059-018-1590-2. Genome Biol. 2018. PMID: 30486838 Free PMC article.
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