bwamem.bib

@article{Langmead:2012fk,
	Author = {Langmead, Ben and Salzberg, Steven L},
	Journal = {Nat Methods},
	Month = {Apr},
	Pages = {357-9},
	Title = {{Fast gapped-read alignment with Bowtie 2}},
	Volume = {9},
	Year = {2012}}

@article{Liu:2012uq,
	Author = {Liu, Yongchao and Schmidt, Bertil},
	Journal = {Bioinformatics},
	Month = {Sep},
	Pages = {i318-i324},
	Title = {Long read alignment based on maximal exact match seeds},
	Volume = {28},
	Year = {2012}}

@article{Li:2010fk,
	Author = {Li, Heng and Durbin, Richard},
	Journal = {Bioinformatics},
	Month = {Mar},
	Pages = {589-95},
	Title = {Fast and accurate long-read alignment with Burrows-Wheeler transform},
	Volume = {26},
	Year = {2010}}

@article{Marco-Sola:2012kx,
	Author = {Marco-Sola, Santiago and others},
	Journal = {Nat Methods},
	Month = {Dec},
	Pages = {1185-8},
	Title = {{The GEM mapper: fast, accurate and versatile alignment by filtration}},
	Volume = {9},
	Year = {2012}}

@article{Li:2012fk,
	Author = {Li, Heng},
	Journal = {Bioinformatics},
	Month = {Jul},
	Pages = {1838-44},
	Title = {{Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly}},
	Volume = {28},
	Year = {2012}}

@article{Altschul:1997vn,
	Author = {Altschul, S F and others},
	Journal = {Nucleic Acids Res},
	Month = {Sep},
	Pages = {3389-402},
	Title = {{Gapped BLAST and PSI-BLAST: a new generation of protein database search programs}},
	Volume = {25},
	Year = {1997}}

@article{Li:2009uq,
	Author = {Li, Heng and Durbin, Richard},
	Journal = {Bioinformatics},
	Month = {Jul},
	Pages = {1754-60},
	Title = {Fast and accurate short read alignment with Burrows-Wheeler transform},
	Volume = {25},
	Year = {2009}}

@article{Shrestha:2013ys,
	Author = {Shrestha, Anish Man Singh and Frith, Martin C},
	Journal = {Bioinformatics},
	Month = {Feb},
	Title = {An Approximate Bayesian Approach to Mapping Paired-End DNA Reads to a Reference Genome},
	Year = {2013}}

@article{Kurtz:2004zr,
	Author = {Kurtz, Stefan and others},
	Journal = {Genome Biol},
	Pages = {R12},
	Title = {Versatile and open software for comparing large genomes},
	Volume = {5},
	Year = {2004}}

@book{Durbin:1998uq,
	Author = {Durbin, Richard and others},
	Publisher = {Cambridge University Press},
	Title = {Biological sequence analysis},
	Year = {1998}}

@article{Farrar:2007hs,
	Author = {Farrar, Michael},
	Journal = {Bioinformatics},
	Month = {Jan},
	Pages = {156-61},
	Title = {Striped Smith-Waterman speeds database searches six times over other SIMD implementations},
	Volume = {23},
	Year = {2007}}

@article{Mu:2012fk,
	Author = {Mu, John C and others},
	Journal = {Bioinformatics},
	Month = {Sep},
	Pages = {2366-73},
	Title = {Fast and accurate read alignment for resequencing},
	Volume = {28},
	Year = {2012}}

@article{Wu:2010uq,
	Author = {Wu, Thomas D and Nacu, Serban},
	Journal = {Bioinformatics},
	Month = {Apr},
	Pages = {873-81},
	Title = {Fast and SNP-tolerant detection of complex variants and splicing in short reads},
	Volume = {26},
	Year = {2010}}

@article{Dobin:2013kx,
	Author = {Dobin, Alexander and others},
	Journal = {Bioinformatics},
	Month = {Jan},
	Pages = {15-21},
	Title = {STAR: ultrafast universal RNA-seq aligner},
	Volume = {29},
	Year = {2013}}

@article{Shrestha:2013aa,
	Author = {Shrestha, Anish Man Singh and Frith, Martin C},
	Journal = {Bioinformatics},
	Month = {Mar},
	Title = {An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome},
	Year = {2013}}