-
2
-
-
84871688621
-
Analysing and interpreting DNA methylation data
-
Bock C. 2012. Analysing and interpreting DNA methylation data. Nature Reviews Genetics 13(10):705–719 DOI 10.1038/nrg3273.
-
(2012)
Nature Reviews Genetics
, vol.13
, Issue.10
, pp. 705-719
-
-
Bock, C.1
-
3
-
-
84930642023
-
An introduction to docker for reproducible research, with examples from the R environment
-
Boettiger C. 2015. An introduction to docker for reproducible research, with examples from the R environment. ACM SIGOPS Operating Systems Review 49(1)71–79 DOI 10.1145/2723872.272388.
-
(2015)
ACM SIGOPS Operating Systems Review
, vol.49
, Issue.1
, pp. 71-79
-
-
Boettiger, C.1
-
4
-
-
84893443187
-
An extensive evaluation of read trimming effects on Illumina NGS data analysis
-
Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM. 2013. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLOS ONE 8(12):e85024 DOI 10.1371/journal.pone.0085024.
-
(2013)
PLOS ONE
, vol.8
, Issue.12
-
-
Del Fabbro, C.1
Scalabrin, S.2
Morgante, M.3
Giorgi, F.M.4
-
5
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
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. Nature Genetics 43(5):491–498 DOI 10.1038/ng.806.
-
(2011)
Nature Genetics
, vol.43
, Issue.5
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
Hartl, C.6
Philippakis, A.A.7
del Angel, G.8
Rivas, M.A.9
Hanna, M.10
McKenna, A.11
Fennell, T.J.12
Kernytsky, A.M.13
Sivachenko, A.Y.14
Cibulskis, K.15
Gabriel, S.B.16
Altshuler, D.17
Daly, M.J.18
-
6
-
-
85017333736
-
Nextflow enables reproducible computational workflows
-
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. 2017. Nextflow enables reproducible computational workflows. Nature Biotechnology 35(4):316–319 DOI 10.1038/nbt.3820.
-
(2017)
Nature Biotechnology
, vol.35
, Issue.4
, pp. 316-319
-
-
Di Tommaso, P.1
Chatzou, M.2
Floden, E.W.3
Barja, P.P.4
Palumbo, E.5
Notredame, C.6
-
7
-
-
84871809302
-
STAR: ultrafast universal RNA-seq aligner
-
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21 DOI 10.1093/bioinformatics/bts635.
-
(2013)
Bioinformatics
, vol.29
, Issue.1
, pp. 15-21
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
Batut, P.7
Chaisson, M.8
Gingeras, T.R.9
-
8
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research 36(16):e105 DOI 10.1093/nar/gkn425.
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.16
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
9
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74.
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 57-74
-
-
-
10
-
-
84988570649
-
MultiQC: summarize analysis results for multiple tools and samples in a single report
-
Ewels P, Magnusson M, Lundin S, Käller M. 2016. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19):3047–3048 DOI 10.1093/bioinformatics/btw354.
-
(2016)
Bioinformatics
, vol.32
, Issue.19
, pp. 3047-3048
-
-
Ewels, P.1
Magnusson, M.2
Lundin, S.3
Käller, M.4
-
12
-
-
84865760395
-
GENCODE: the reference human genome annotation for The ENCODE Project
-
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I,van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. 2012. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research 22(9):1760–1774 DOI 10.1101/gr.135350.111.
-
(2012)
Genome Research
, vol.22
, Issue.9
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
Aken, B.L.7
Barrell, D.8
Zadissa, A.9
Searle, S.10
Barnes, I.11
Bignell, A.12
Boychenko, V.13
Hunt, T.14
Kay, M.15
Mukherjee, G.16
Rajan, J.17
Despacio-Reyes, G.18
Saunders, G.19
Steward, C.20
Harte, R.21
Lin, M.22
Howald, C.23
Tanzer, A.24
Derrien, T.25
Chrast, J.26
Walters, N.27
Balasubramanian, S.28
Pei, B.29
Tress, M.30
Rodriguez, J.M.31
Ezkurdia, I.32
van Baren, J.33
Brent, M.34
Haussler, D.35
Kellis, M.36
Valencia, A.37
Reymond, A.38
Gerstein, M.39
Guigó, R.40
Hubbard, T.J.41
more..
-
13
-
-
84857145150
-
ART: a next-generation sequencing read simulator
-
Huang W, Li L, Myers JR, Marth GT. 2012. ART: a next-generation sequencing read simulator. Bioinformatics 28(4):593–594 DOI 10.1093/bioinformatics/btr708.
-
(2012)
Bioinformatics
, vol.28
, Issue.4
, pp. 593-594
-
-
Huang, W.1
Li, L.2
Myers, J.R.3
Marth, G.T.4
-
14
-
-
84903513963
-
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
-
Jiang H, Lei R, Ding S-W, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15(1):182 DOI 10.1186/1471-2105-15-182.
-
(2014)
BMC Bioinformatics
, vol.15
, Issue.1
-
-
Jiang, H.1
Lei, R.2
Ding, S.-W.3
Zhu, S.4
-
15
-
-
85020173038
-
Singularity linux application and environment containers for science
-
Zenodo
-
Kurtzer GM. 2016. Singularity linux application and environment containers for science. Version: 2.1.2. Zenodo DOI 10.5281/zenodo.60736.
-
(2016)
Version: 2.1.2.
-
-
GM, K.1
-
16
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1):10–12 DOI 10.14806/ej.17.1.200.
-
(2011)
EMBnet.journal
, vol.17
, Issue.1
, pp. 10-12
-
-
Martin, M.1
-
17
-
-
85051947642
-
Algorithms and tools for the analysis of high-throughput DNA sequencing data
-
PhD thesis, Technical University of Dortmund
-
Martin M. 2013. Algorithms and tools for the analysis of high-throughput DNA sequencing data. PhD thesis, Technical University of Dortmund.
-
(2013)
-
-
Martin, M.1
-
19
-
-
84958153152
-
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
-
Schubert M, Lindgreen S, Orlando L. 2016. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes 9:88 DOI 10.1186/s13104-016-1900-2.
-
(2016)
BMC Research Notes
, vol.9
-
-
Schubert, M.1
Lindgreen, S.2
Orlando, L.3
-
20
-
-
84968912174
-
SeqPurge: highly-sensitive adapter trimming for paired-end NGS data
-
Sturm M, Schroeder C, Bauer P. 2016. SeqPurge: highly-sensitive adapter trimming for paired-end NGS data. BMC Bioinformatics 17(1):208 DOI 10.1186/s12859-016-1069-7.
-
(2016)
BMC Bioinformatics
, vol.17
, Issue.1
-
-
Sturm, M.1
Schroeder, C.2
Bauer, P.3
-
21
-
-
0000386785
-
Finding approximate patterns in strings
-
Ukkonen E. 1985. Finding approximate patterns in strings. Journal of Algorithms 6(1):132–137 DOI 10.1016/0196-6774(85)90023-9.
-
(1985)
Journal of Algorithms
, vol.6
, Issue.1
, pp. 132-137
-
-
Ukkonen, E.1
-
22
-
-
84879446930
-
Estimation of sequencing error rates in short reads
-
Wang XV, Blades N, Ding J, Sultana R, Parmigiani G. 2012. Estimation of sequencing error rates in short reads. BMC Bioinformatics 13(1):185 DOI 10.1186/1471-2105-13-185.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.1
, pp. 185
-
-
Wang, X.V.1
Blades, N.2
Ding, J.3
Sultana, R.4
Parmigiani, G.5
|