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[GalaxyCodeBases.git] / BioInfo / BS-Seq / bwa-meth / paper / document.bib
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1 @article{bsmap,
2 title = {{BSMAP:} whole genome bisulfite sequence {MAPping} program},
3 volume = {10},
4 number = {1},
5 journal = {{BMC} bioinformatics},
6 author = {Xi, Yuanxin and Li, Wei},
7 year = {2009},
8 pages = {232}
9 },
11 @article{bsmooth,
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},
15 volume={13},
16 number={10},
17 pages={R83},
18 year={2012}
21 @article{shrestha,
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},
25 volume={29},
26 number={8},
27 pages={965--972},
28 year={2013},
29 publisher={Oxford Univ Press}
32 @article{gsnap,
33 title = {Fast and {SNP-tolerant} detection of complex variants and splicing in short reads},
34 volume = {26},
35 number = {7},
36 journal = {Bioinformatics},
37 author = {Wu, Thomas D and Nacu, Serban},
38 year = {2010},
39 pages = {873-881}
42 @article{krueger2011,
43 title = {Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications},
44 volume = {27},
45 number = {11},
46 journal = {Bioinformatics},
47 author = {Krueger, Felix and Andrews, Simon R},
48 year = {2011},
49 pages = {1571-1572}
52 @article{methylcoder,
53 title = {{MethylCoder:} software pipeline for bisulfite-treated sequences},
54 volume = {27},
55 number = {17},
56 journal = {Bioinformatics},
57 author = {Pedersen, Brent S and Hsieh, Tzung-Fu and Ibarra, Christian and Fischer, Robert L},
58 year = {2011},
59 pages = {2435-2436}
62 @article{encode,
63 title = {An integrated encyclopedia of {DNA} elements in the human genome},
64 volume = {489},
65 copyright = {2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
66 issn = {0028-0836},
67 url = {http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html},
68 doi = {10.1038/nature11247},
69 language = {en},
70 number = {7414},
71 urldate = {2013-09-30},
72 journal = {Nature},
73 author = {Consortium, The ENCODE Project},
74 month = sep,
75 year = {2012},
76 keywords = {Genetics, Genomics, Molecular biology},
77 pages = {57--74},
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}
81 @article{frithlast,
82 title = {A mostly traditional approach improves alignment of bisulfite-converted {DNA}},
83 volume = {40},
84 number = {13},
85 journal = {Nucleic acids research},
86 author = {Frith, Martin C and Mori, Ryota and Asai, Kiyoshi},
87 year = {2012},
88 pages = {e100-e100}
91 @article{bissnp,
92 title = {Bis-{SNP:} Combined {DNA} methylation and {SNP} calling for Bisulfite-seq data},
93 volume = {13},
94 number = {7},
95 journal = {Genome Biol},
96 author = {Liu, Yaping and Siegmund, Kimberly D and Laird, Peter W and Berman, Benjamin P and others},
97 year = {2012},
98 pages = {R61}
101 @article{bwamem,
102 title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
103 volume = {},
104 number = {},
105 journal = {{arXiv} preprint arXiv:1303.3997},
106 author = {Li, Heng},
107 year = {2013}
110 @article{GATK,
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},
114 volume={20},
115 number={9},
116 pages={1297--1303},
117 year={2010},
118 publisher={Cold Spring Harbor Lab}
121 @misc{sickle2014,
122 title = {sickle},
123 url = {https://github.com/najoshi/sickle},
124 abstract = {trim sequencing reads},
125 month = dec,
126 year = {2014}
130 @article{cnmops,
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},
134 volume={40},
135 number={9},
136 pages={e69--e69},
137 year={2012},
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},
146 volume={5},
147 number={10},
148 pages={R80},
149 year={2004},
150 publisher={BioMed Central Ltd}