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citations.txt
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Software Citations
The pipelines uses the following software:
Gordon A, Hannon G. 2010. Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab cshl edu/fastx_toolkit.
Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841-842.
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297-1303.
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. 2002. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline, Current Protocols in Bioinformatics doi:10.1002/0471250953.bi1110s43. John Wiley & Sons, Inc.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14:R36.
Chikhi R, Medvedev P. 2014. Informed and automated k-mer size selection for genome assembly. Bioinformatics 30:31-37.
Bushnell B. BBMap short read aligner. URL http://sourceforge net/projects/bbmap.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647-1649.
Pierre L. JVarkit: java-based utilities for Bioinformatics.
Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, Cardle L, et al. Using Tablet for visual exploration of second-generation sequencing data. Briefings in Bioinformatics. 2013;14(2):193-202. doi: 10.1093/bib/bbs012.
Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, et al. Tablet—next generation sequence assembly visualization. Bioinformatics (Oxford, England). 2010;26(3):401-2. doi: 10.1093/bioinformatics/btp666. PubMed PMID: PMC2815658.
Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics (Oxford, England). 2004;20(2):289-90. doi: 10.1093/bioinformatics/btg412.
Team RC. R: A language and environment for statistical computing. 2013.
MacQueen J, editor Some methods for classification and analysis of multivariate observations. Proceedings of the fifth Berkeley symposium on mathematical statistics and probability; 1967: Oakland, CA, USA.
Lloyd S. Least squares quantization in PCM. IEEE transactions on information theory. 1982;28(2):129-37.
Hartigan JA, Wong MA. Algorithm AS 136: A k-means clustering algorithm. Journal of the Royal Statistical Society Series C (Applied Statistics). 1979;28(1):100-8.
Forgy EW. Cluster analysis of multivariate data: efficiency versus interpretability of classifications. Biometrics. 1965;21:768-9.
Fraley C, Raftery AE. MCLUST: Software for model-based cluster analysis. Journal of Classification. 1999;16(2):297-306.
Fraley C, Raftery AE. MCLUST version 3: an R package for normal mixture modeling and model-based clustering. DTIC Document, 2006.