-
1
-
-
84857524013
-
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
-
Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, et al. (2012) Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data. PloS One 7: e31386.
-
(2012)
PloS One
, vol.7
-
-
Mende, D.R.1
Waller, A.S.2
Sunagawa, S.3
Järvelin, A.I.4
Chan, M.M.5
-
2
-
-
79952422304
-
Quality control and preprocessing of metagenomic datasets
-
Schmieder R, Edwards R, (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863-864.
-
(2011)
Bioinformatics
, vol.27
, pp. 863-864
-
-
Schmieder, R.1
Edwards, R.2
-
3
-
-
84856468953
-
NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data
-
Patel RK, Jain M, (2012) NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data. PloS One 7: e30619.
-
(2012)
PloS One
, vol.7
-
-
Patel, R.K.1
Jain, M.2
-
4
-
-
79952390994
-
Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
-
Schmieder R, Edwards R, (2011) Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets. PloS One 6: e17288.
-
(2011)
PloS One
, vol.6
-
-
Schmieder, R.1
Edwards, R.2
-
5
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
6
-
-
84867307868
-
Parallel-META: efficient metagenomic data analysis based on high-performance computation
-
Su X, Xu J, Ning K, (2012) Parallel-META: efficient metagenomic data analysis based on high-performance computation. BMC Systems Biology 6: S16.
-
(2012)
BMC Systems Biology
, vol.6
-
-
Su, X.1
Xu, J.2
Ning, K.3
-
7
-
-
58149200948
-
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
-
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research 37: D141-D145.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
-
8
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and environmental microbiology 72: 5069-5072.
-
(2006)
Applied and Environmental Microbiology
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
-
9
-
-
37549027613
-
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 35: 7188-7196.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.M.4
Ludwig, W.5
-
10
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E, (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
-
(2008)
Genome Research
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
11
-
-
33645161645
-
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
-
Stanke M, Schöffmann O, Morgenstern B, Waack S, (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC bioinformatics 7: 62.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 62
-
-
Stanke, M.1
Schöffmann, O.2
Morgenstern, B.3
Waack, S.4
-
12
-
-
84861760530
-
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng Y, Leung HCM, Yiu SM, Chin FYL, (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420-1428.
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
14
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
15
-
-
67650711615
-
SOAP2: an improved ultrafast tool for short read alignment
-
Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
Lam, T.W.4
Yiu, S.M.5
-
16
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
-
17
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Available:. Accessed 31 Jan 2013
-
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 1. Available: http://journal.embnet.org/index.php/embnetjournal/article/view/200. Accessed 31 Jan 2013.
-
(2011)
EMBnet.journal
, vol.17
, pp. 1
-
-
Martin, M.1
-
18
-
-
84856498057
-
DNA methylome analysis using short bisulfite sequencing data
-
Krueger F, Kreck B, Franke A, Andrews SR, (2012) DNA methylome analysis using short bisulfite sequencing data. Nat Meth 9: 145-151.
-
(2012)
Nat Meth
, vol.9
, pp. 145-151
-
-
Krueger, F.1
Kreck, B.2
Franke, A.3
Andrews, S.R.4
|