-
1
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
-
doi: 10 1186/gb-2011-12-2-r18
-
Aird, D , Ross, M G , Chen, W -S , Danielsson, M , Fennell, T , Russ, C , et al (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Genome Biol 12:R18 doi: 10 1186/gb-2011-12-2-r18
-
(2011)
Genome Biol
, vol.12
-
-
Aird, D.1
Ross, M.G.2
Chen, W.-S.3
Danielsson, M.4
Fennell, T.5
Russ, C.6
-
2
-
-
84905670958
-
-
FASTQC Package Available online at:
-
Andrews, S (2010a) FASTQC Package Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-
(2010)
-
-
Andrews, S.1
-
3
-
-
84905661815
-
-
Fastq-screen Package Available online at:
-
Andrews, S (2010b) Fastq-screen Package Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
-
(2010)
-
-
Andrews, S.1
-
4
-
-
84868193189
-
Optical properties of chitin and chitosan biopolymers with application to structural color analysis
-
doi: 10 1016/j optmat 2012 07 024
-
Azofeifa, D E , Arguedas, H J , and Vargas, W E (2012) Optical properties of chitin and chitosan biopolymers with application to structural color analysis Opt Mater 35, 175-183 doi: 10 1016/j optmat 2012 07 024
-
(2012)
Opt Mater
, vol.35
, pp. 175-183
-
-
Azofeifa, D.E.1
Arguedas, H.J.2
Vargas, W.E.3
-
5
-
-
77957151956
-
Solexa QA: at-a-glance quality assessment of Illumina second-generation sequencing data
-
doi: 10 1186/1471-2105-11-485
-
Cox, M P , Peterson, D A , and Biggs, P J (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data BMC Bioinformatics 11:485 doi: 10 1186/1471-2105-11-485
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 485
-
-
Cox, M.P.1
Peterson, D.A.2
Biggs, P.J.3
-
6
-
-
84883492771
-
Kraken: a set of tools for quality control and analysis of high-throughput sequence data
-
doi: 10 1016/j ymeth 2013 06 027
-
Davis, M P A , van Dongen, S , Abreu-Goodger, C , Bartonicek, N , and Enright, A J (2013) Kraken: a set of tools for quality control and analysis of high-throughput sequence data Methods 63, 41-49 doi: 10 1016/j ymeth 2013 06 027
-
(2013)
Methods
, vol.63
, pp. 41-49
-
-
Davis, M.P.A.1
van Dongen, S.2
Abreu-Goodger, C.3
Bartonicek, N.4
Enright, A.J.5
-
7
-
-
84861743958
-
RNA-SeQC: RNA-seq metrics for quality control and process optimization
-
doi: 10 1093/bioinformatics/bts196
-
DeLuca, D S , Levin, J Z , Sivachenko, A , Fennell, T , Nazaire, M D , Williams, C , et al (2012) RNA-SeQC: RNA-seq metrics for quality control and process optimization Bioinformatics 28, 1530-1532 doi: 10 1093/bioinformatics/bts196
-
(2012)
Bioinformatics
, vol.28
, pp. 1530-1532
-
-
DeLuca, D.S.1
Levin, J.Z.2
Sivachenko, A.3
Fennell, T.4
Nazaire, M.D.5
Williams, C.6
-
8
-
-
0036081355
-
Gene expression omnibus: NCBI gene expression and hybridization array data repository
-
doi: 10 1093/nar/30 1 207
-
Edgar, R (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res 30, 207-210 doi: 10 1093/nar/30 1 207
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 207-210
-
-
Edgar, R.1
-
9
-
-
80051836774
-
DNA extraction columns contaminated with murine sequences
-
doi: 10 1371/journal pone 0023484
-
Erlwein, O , Robinson, M J , Dustan, S , Weber, J , Kaye, S , and McClure, M O (2011) DNA extraction columns contaminated with murine sequences PLoS ONE 6:e23484 doi: 10 1371/journal pone 0023484
-
(2011)
PLoS ONE
, vol.6
-
-
Erlwein, O.1
Robinson, M.J.2
Dustan, S.3
Weber, J.4
Kaye, S.5
McClure, M.O.6
-
10
-
-
0038156059
-
Contamination of qiagen DNA extraction kits with legionella DNA
-
doi: 10 1128/JCM 41 7 3452-3453 2003
-
Evans, G E , Murdoch, D R , Anderson, T P , Potter, H C , George, P M , and Chambers, S T (2003) Contamination of qiagen DNA extraction kits with legionella DNA J Clin Microbiol 41, 3452-3453 doi: 10 1128/JCM 41 7 3452-3453 2003
-
(2003)
J Clin Microbiol
, vol.41
, pp. 3452-3453
-
-
Evans, G.E.1
Murdoch, D.R.2
Anderson, T.P.3
Potter, H.C.4
George, P.M.5
Chambers, S.T.6
-
11
-
-
43449108562
-
The minimum information about a genome sequence (MIGS) specification
-
doi: 10 1038/nbt1360
-
Field, D , Garrity, G , Gray, T , Morrison, N , Selengut, J , Sterk, P , et al (2008) The minimum information about a genome sequence (MIGS) specification Nat Biotechnol 26, 541-547 doi: 10 1038/nbt1360
-
(2008)
Nat Biotechnol
, vol.26
, pp. 541-547
-
-
Field, D.1
Garrity, G.2
Gray, T.3
Morrison, N.4
Selengut, J.5
Sterk, P.6
-
12
-
-
84870422798
-
Qualimap: evaluating next-generation sequencing alignment data
-
doi: 10 1093/bioinformatics/bts503
-
García-Alcalde, F , Okonechnikov, K , Carbonell, J , Cruz, L M , Götz, S , Tarazona, S , et al (2012) Qualimap: evaluating next-generation sequencing alignment data Bioinformatics 28, 2678-2679 doi: 10 1093/bioinformatics/bts503
-
(2012)
Bioinformatics
, vol.28
, pp. 2678-2679
-
-
García-Alcalde, F.1
Okonechnikov, K.2
Carbonell, J.3
Cruz, L.M.4
Götz, S.5
Tarazona, S.6
-
13
-
-
77955801615
-
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
doi: 10 1186/gb-2010-11-8-r86
-
Goecks, J , Nekrutenko, A , and Taylor, J (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol 11:R86 doi: 10 1186/gb-2010-11-8-r86
-
(2010)
Genome Biol
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
14
-
-
84905670956
-
-
FASTX-toolkit Package Available online at:
-
Hannon, G (2010) FASTX-toolkit Package Available online at: http://hannonlab.cshl.edu/fastx_toolkit/
-
(2010)
-
-
Hannon, G.1
-
15
-
-
77955883388
-
Biases in Illumina transcriptome sequencing caused by random hexamer priming
-
doi: 10 1093/nar/gkq224
-
Hansen, K D , Brenner, S E , and Dudoit, S (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming Nucleic Acids Res 38, e131 doi: 10 1093/nar/gkq224
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Hansen, K.D.1
Brenner, S.E.2
Dudoit, S.3
-
16
-
-
84891349082
-
A poor man's BLASTX-high-throughput metagenomic protein database search using PAUDA
-
doi: 10.1093/bioinformatics/btt254
-
Huson, D H , and Xie, C (2014) A poor man's BLASTX-high-throughput metagenomic protein database search using PAUDA Bioinformatics 30, 38-39 doi: 10 1093/bioinformatics/btt254
-
(2014)
Bioinformatics
, vol.30
, pp. 38-39
-
-
Huson, D.H.1
Xie, C.2
-
17
-
-
28644452204
-
Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces
-
doi: 10 1093/nar/gni054
-
Imbeaud, S , Graudens, E , Boulanger, V , Barlet, X , Zaborski, P , Eveno, E , et al (2005) Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces Nucl Acids Res 33, e56 doi: 10 1093/nar/gni054
-
(2005)
Nucl Acids Res
, vol.33
-
-
Imbeaud, S.1
Graudens, E.2
Boulanger, V.3
Barlet, X.4
Zaborski, P.5
Eveno, E.6
-
18
-
-
80052521697
-
Synthetic spike-in standards for RNA-seq experiments
-
doi: 10 1101/gr 121095 111
-
Jiang, L , Schlesinger, F , Davis, C A , Zhang, Y , Li, R , Salit, M , et al (2011) Synthetic spike-in standards for RNA-seq experiments Genome Res 21, 1543-1551 doi: 10 1101/gr 121095 111
-
(2011)
Genome Res
, vol.21
, pp. 1543-1551
-
-
Jiang, L.1
Schlesinger, F.2
Davis, C.A.3
Zhang, Y.4
Li, R.5
Salit, M.6
-
19
-
-
84897110016
-
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots
-
doi: 10 3389/fgene 2013 00237
-
Kumar, S , Jones, M , Koutsovoulos, G , Clarke, M , and Blaxter, M (2013) Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots Front Genet 4:237 doi: 10 3389/fgene 2013 00237
-
(2013)
Front Genet
, vol.4
, pp. 237
-
-
Kumar, S.1
Jones, M.2
Koutsovoulos, G.3
Clarke, M.4
Blaxter, M.5
-
20
-
-
77953001848
-
Application of spectroscopic methods for structural analysis of chitin and chitosan
-
doi: 10 3390/md8051567
-
Kumirska, J , Cerwicka, M , Kaczyñski, Z , Bychowska, A , Brzozowski, K , Thöming, J , et al (2010) Application of spectroscopic methods for structural analysis of chitin and chitosan Mar Drugs 8, 1567-1636 doi: 10 3390/md8051567
-
(2010)
Mar Drugs
, vol.8
, pp. 1567-1636
-
-
Kumirska, J.1
Cerwicka, M.2
Kaczyñski, Z.3
Bychowska, A.4
Brzozowski, K.5
Thöming, J.6
-
21
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
doi: 10 1186/gb-2009-10-3-r25
-
Langmead, B , Trapnell, C , Pop, M , and Salzberg, S L (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol 10:R25 doi: 10 1186/gb-2009-10-3-r25
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
22
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
doi: 10 1093/bioinformatics/btp324
-
Li, H , and Durbin, R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25, 1754-1760 doi: 10 1093/bioinformatics/btp324
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
23
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
doi: 10 1093/bioinformatics/btp352
-
Li, H , Handsaker, B , Wysoker, A , Fennell, T , Ruan, J , Homer, N , et al (2009) The sequence alignment/map format and SAMtools Bioinformatics 25, 2078-2079 doi: 10 1093/bioinformatics/btp352
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
24
-
-
49549112511
-
Database indexing for production MegaBLAST searches
-
doi: 10 1093/bioinformatics/btn322
-
Morgulis, A , Coulouris, G , Raytselis, Y , Madden, T L , Agarwala, R , and Schäffer, A A (2008) Database indexing for production MegaBLAST searches Bioinformatics 24, 1757-1764 doi: 10 1093/bioinformatics/btn322
-
(2008)
Bioinformatics
, vol.24
, pp. 1757-1764
-
-
Morgulis, A.1
Coulouris, G.2
Raytselis, Y.3
Madden, T.L.4
Agarwala, R.5
Schäffer, A.A.6
-
25
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
doi: 10 1038/nmeth 1226
-
Mortazavi, A , Williams, B A , McCue, K , Schaeffer, L , and Wold, B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat Methods 5, 621-628 doi: 10 1038/nmeth 1226
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
26
-
-
23944504645
-
RNA Integrity Number (RIN) - Standardization of RNA Quality Control
-
Agilent publication Available online at:
-
Mueller, O , Lightfoot, S , and Schroeder, A (2004) RNA Integrity Number (RIN) - Standardization of RNA Quality Control Agilent publication Available online at: https://www.chem.agilent.com/Library/applications/5989-1165EN.pdf
-
(2004)
-
-
Mueller, O.1
Lightfoot, S.2
Schroeder, A.3
-
27
-
-
84856468953
-
NGS QC toolkit: a toolkit for quality control of next generation sequencing data
-
doi: 10 1371/journal pone 0030619
-
Patel, R K , and Jain, M (2012) NGS QC toolkit: a toolkit for quality control of next generation sequencing data PLoS ONE 7:e30619 doi: 10 1371/journal pone 0030619
-
(2012)
PLoS ONE
, vol.7
-
-
Patel, R.K.1
Jain, M.2
-
28
-
-
84856448155
-
Optimal enzymes for amplifying sequencing libraries
-
doi: 10 1038/nmeth 1814
-
Quai, M A , Otto, T D , Gu, Y , Harris, S R , Skelly, T F , McQuillan, J A , et al (2012) Optimal enzymes for amplifying sequencing libraries Nat Methods 9, 10-11 doi: 10 1038/nmeth 1814
-
(2012)
Nat Methods
, vol.9
, pp. 10-11
-
-
Quai, M.A.1
Otto, T.D.2
Gu, Y.3
Harris, S.R.4
Skelly, T.F.5
McQuillan, J.A.6
-
29
-
-
0003602325
-
The MD5 Message-Digest Algorithm
-
RFC 1321 Fremont, CA: Internet Engineering Task Force
-
Rivest, R (1992) The MD5 Message-Digest Algorithm RFC 1321 Fremont, CA: Internet Engineering Task Force
-
(1992)
-
-
Rivest, R.1
-
30
-
-
84878234942
-
Characterizing and measuring bias in sequence data
-
doi: 10 1186/gb-2013-14-5-r51
-
Ross, M G , Russ, C , Costello, M , Hollinger, A , Lennon, N J , Hegarty, R , et al (2013) Characterizing and measuring bias in sequence data Genome Biol 14:R51 doi: 10 1186/gb-2013-14-5-r51
-
(2013)
Genome Biol
, vol.14
-
-
Ross, M.G.1
Russ, C.2
Costello, M.3
Hollinger, A.4
Lennon, N.J.5
Hegarty, R.6
-
31
-
-
33645241407
-
The RIN: an RNA integrity number for assigning integrity values to RNA measurements
-
doi: 10 1186/1471-2199-7-3
-
Schroeder, A , Mueller, O , Stocker, S , Salowsky, R , Leiber, M , Gassmann, M , et al (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements BMC Mol Biol 7:3 doi: 10 1186/1471-2199-7-3
-
(2006)
BMC Mol Biol
, vol.7
, pp. 3
-
-
Schroeder, A.1
Mueller, O.2
Stocker, S.3
Salowsky, R.4
Leiber, M.5
Gassmann, M.6
-
32
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
doi: 10 1038/nbt 1621
-
Trapnell, C , Williams, B A , Pertea, G , Mortazavi, A , Kwan, G , van Baren, M J , et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat Biotechnol 28, 511-515 doi: 10 1038/nbt 1621
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
-
33
-
-
34548293679
-
Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
doi: 10 1128/AEM 00062-07
-
Wang, Q , Garrity, G M , Tiedje, J M , and Cole, J R (2007) Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy Appl Environ Microbiol 73, 5261-5267 doi: 10 1128/AEM 00062-07
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
34
-
-
38549092091
-
Database resources of the national center for biotechnology information
-
doi: 10 1093/nar/gkm1000
-
Wheeler, D L , Barrett, T , Benson, D A , Bryant, S H , Canese, K , Chetvernin, V , et al (2008) Database resources of the national center for biotechnology information Nucleic Acids Res 36, D13-D21 doi: 10 1093/nar/gkm1000
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
-
35
-
-
78649281091
-
Why does insect R N A look degraded?
-
doi: 10 1673/031 010 14119
-
Winnebeck, E C , Millar, C D , and Warman, G R (2010) Why does insect RNA look degraded? J Insect Sci 10:159 doi: 10 1673/031 010 14119
-
(2010)
J Insect Sci
, vol.10
, pp. 159
-
-
Winnebeck, E.C.1
Millar, C.D.2
Warman, G.R.3
-
36
-
-
84873041419
-
HTQC: a fast quality control toolkit for Illumina sequencing data
-
doi: 10 1186/1471-2105-14-33
-
Yang, X , Liu, D , Liu, F , Wu, J , Zou, J , Xiao, X , et al (2013) HTQC: a fast quality control toolkit for Illumina sequencing data BMC Bioinformatics 14:33 doi: 10 1186/1471-2105-14-33
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 33
-
-
Yang, X.1
Liu, D.2
Liu, F.3
Wu, J.4
Zou, J.5
Xiao, X.6
-
37
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
doi: 10 1101/gr 074492 107
-
Zerbino, D R , and Birney, E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs Genome Res 18, 821-829 doi: 10 1101/gr 074492 107
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney E.2
3
-
38
-
-
84875647144
-
QC-chain: fast and holistic quality control method for next-generation sequencing data
-
doi: 10 1371/journal pone 0060234
-
Zhou, Q , Su, X , Wang, A , Xu, J , and Ning, K (2013) QC-chain: fast and holistic quality control method for next-generation sequencing data PLoS ONE 8:e60234 doi: 10 1371/journal pone 0060234
-
(2013)
PLoS ONE
, vol.8
-
-
Zhou, Q.1
Su, X.2
Wang, A.3
Xu, J.4
Ning, K.5
|