2 title = {{BSMAP
:} whole genome bisulfite sequence
{MAPping
} program
},
5 journal = {{BMC
} bioinformatics
},
6 author = {Xi
, Yuanxin and Li
, Wei
},
12 title={BSmooth
: from whole genome bisulfite sequencing reads to differentially methylated regions
},
13 author={Hansen
, Kasper D and Langmead
, Benjamin and Irizarry
, Rafael A and others
},
14 journal={Genome Biol
},
22 title={An approximate Bayesian approach for mapping paired
-end DNA reads to a reference genome
},
23 author={Shrestha
, Anish Man Singh and Frith
, Martin C
},
24 journal={Bioinformatics
},
29 publisher={Oxford Univ Press
}
33 title = {Fast and
{SNP
-tolerant
} detection of complex variants and splicing in short reads
},
36 journal = {Bioinformatics
},
37 author = {Wu
, Thomas D and Nacu
, Serban
},
43 title = {Bismark
: a flexible aligner and methylation caller for Bisulfite
-Seq applications
},
46 journal = {Bioinformatics
},
47 author = {Krueger
, Felix and Andrews
, Simon R
},
53 title = {{MethylCoder
:} software pipeline for bisulfite
-treated sequences
},
56 journal = {Bioinformatics
},
57 author = {Pedersen
, Brent S and Hsieh
, Tzung
-Fu and Ibarra
, Christian and Fischer
, Robert L
},
63 title = {An integrated encyclopedia of
{DNA
} elements in the human genome
},
65 copyright
= {2012 Nature Publishing Group
, a division of Macmillan Publishers Limited. All Rights Reserved.
},
67 url
= {http
://www.nature.com
/nature
/journal/v489
/n7414
/full
/nature11247.html
},
68 doi
= {10.1038/nature11247
},
71 urldate
= {2013-09-30},
73 author = {Consortium
, The ENCODE Project
},
76 keywords = {Genetics
, Genomics
, Molecular biology
},
78 file
= {Full Text PDF
:/home
/brentp
/.mozilla
/firefox
/c4oq4z0a.default
/zotero
/storage
/QFFRNF6Q
/Consortium
- 2012 - An integrated encyclopedia of DNA elements in the .pdf
:application
/pdf
;Snapshot
:/home
/brentp
/.mozilla
/firefox
/c4oq4z0a.default
/zotero
/storage
/9TE93MUS
/nature11247.html
:text
/html
}
82 title = {A mostly traditional approach improves alignment of bisulfite
-converted
{DNA
}},
85 journal = {Nucleic acids research
},
86 author = {Frith
, Martin C and Mori
, Ryota and Asai
, Kiyoshi
},
92 title = {Bis
-{SNP
:} Combined
{DNA
} methylation and
{SNP
} calling for Bisulfite
-seq data
},
95 journal = {Genome Biol
},
96 author = {Liu
, Yaping and Siegmund
, Kimberly D and Laird
, Peter W and Berman
, Benjamin P and others
},
102 title = {Aligning sequence reads
, clone sequences and assembly contigs with BWA
-MEM
},
105 journal = {{arXiv
} preprint arXiv
:1303.3997},
111 title={The Genome Analysis Toolkit
: a MapReduce framework for analyzing next
-generation DNA sequencing data
},
112 author={McKenna
, Aaron and Hanna
, Matthew and Banks
, Eric and Sivachenko
, Andrey and Cibulskis
, Kristian and Kernytsky
, Andrew and Garimella
, Kiran and Altshuler
, David and Gabriel
, Stacey and Daly
, Mark and others
},
113 journal={Genome research
},
118 publisher={Cold Spring Harbor Lab
}
123 url
= {https
://github.com
/najoshi
/sickle
},
124 abstract = {trim sequencing reads
},
131 title={cn. MOPS
: mixture of Poissons for discovering copy
number variations in next
-generation sequencing data with a low false discovery rate
},
132 author={Klambauer
, G
{\"u
}nter and Schwarzbauer
, Karin and Mayr
, Andreas and Clevert
, Djork
-Arn
{\'e
} and Mitterecker
, Andreas and Bodenhofer
, Ulrich and Hochreiter
, Sepp
},
133 journal={Nucleic Acids Research
},
138 publisher={Oxford Univ Press
}
142 @article
{bioconductor
,
143 title={Bioconductor
: open software development for computational biology and bioinformatics
},
144 author={Gentleman
, Robert C and Carey
, Vincent J and Bates
, Douglas M and Bolstad
, Ben and Dettling
, Marcel and Dudoit
, Sandrine and Ellis
, Byron and Gautier
, Laurent and Ge
, Yongchao and Gentry
, Jeff and others
},
145 journal={Genome biology
},
150 publisher={BioMed Central Ltd
}