-
1
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-95 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
2
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
3
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-303 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
4
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-9 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
5
-
-
84923798102
-
An analytical framework for optimizing variant discovery from personal genomes
-
Highnam, G. et al. An analytical framework for optimizing variant discovery from personal genomes. Nat. Commun. 6, 6275 (2015).
-
(2015)
Nat. Commun.
, vol.6
, pp. 6275
-
-
Highnam, G.1
-
6
-
-
84897387657
-
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
-
Zook, J. M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246-251 (2014).
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 246-251
-
-
Zook, J.M.1
-
7
-
-
84875312984
-
Low concordance of multiple variant-calling pipelines: Practical implications for exome and genome sequencing
-
O'Rawe, J. et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med 5, 28 (2013).
-
(2013)
Genome Med
, vol.5
, pp. 28
-
-
O'Rawe, J.1
-
8
-
-
84907687102
-
Validation and assessment of variant calling pipelines for next-generation sequencing
-
Pirooznia, M. et al. Validation and assessment of variant calling pipelines for next-generation sequencing. Hum. Genomics 8, 14 (2014).
-
(2014)
Hum. Genomics
, vol.8
, pp. 14
-
-
Pirooznia, M.1
-
9
-
-
84913546864
-
Toward better understanding of artifacts in variant calling from high-coverage samples
-
Li, H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 30, 2843-51 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2843-2851
-
-
Li, H.1
-
10
-
-
84855989774
-
Fast computation and applications of genome mappability
-
Derrien, T. et al. Fast computation and applications of genome mappability. PLoS One 7 (2012).
-
(2012)
PLoS One
, vol.7
-
-
Derrien, T.1
-
11
-
-
84864326252
-
Genomic dark matter: The reliability of short read mapping illustrated by the genome mappability score
-
Lee, H. & Schatz, M. C. Genomic dark matter: The reliability of short read mapping illustrated by the genome mappability score. Bioinformatics 28, 2097-2105 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 2097-2105
-
-
Lee, H.1
Schatz, M.C.2
-
12
-
-
84922584295
-
Comprehensive variation discovery in single human genomes
-
Weisenfeld, N. I. et al. Comprehensive variation discovery in single human genomes. Nat. Genet. 46, 1350-5 (2014).
-
(2014)
Nat. Genet.
, vol.46
, pp. 1350-1355
-
-
Weisenfeld, N.I.1
-
13
-
-
84901844488
-
K-mer natural vector and its application to the phylogenetic analysis of genetic sequences
-
Wen, J., Chan, R. H. F., Yau, S.-C., He, R. L. & Yau, S. S. T. K-mer natural vector and its application to the phylogenetic analysis of genetic sequences. Gene 546, 25-34 (2014).
-
(2014)
Gene
, vol.546
, pp. 25-34
-
-
Wen, J.1
Chan, R.H.F.2
Yau, S.-C.3
He, R.L.4
Yau, S.S.T.5
-
15
-
-
84927731921
-
Andi: Fast and accurate estimation of evolutionary distances between closely related genomes
-
Haubold, B., Klötzl, F. & Pfaffelhuber, P. andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics 31, 1169-75 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 1169-1175
-
-
Haubold, B.1
Klötzl, F.2
Pfaffelhuber, P.3
-
16
-
-
84891529869
-
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples
-
Hasman, H. et al. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J. Clin. Microbiol. 52, 139-46 (2014).
-
(2014)
J. Clin. Microbiol.
, vol.52
, pp. 139-146
-
-
Hasman, H.1
-
17
-
-
84899090573
-
Kraken: Ultrafast metagenomic sequence classification using exact alignments
-
Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. R46
-
-
Wood, D.E.1
Salzberg, S.L.2
-
19
-
-
84965186660
-
Lighter: Fast and memory-efficient sequencing error correction without counting
-
Song, L., Florea, L. & Langmead, B. Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol. 15, 509 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 509
-
-
Song, L.1
Florea, L.2
Langmead, B.3
-
20
-
-
84939173793
-
QuorUM: An Error Corrector for Illumina Reads
-
Marçais, G., Yorke, J. A. & Zimin, A. QuorUM: An Error Corrector for Illumina Reads. PLoS One 10, e0130821 (2015).
-
(2015)
PLoS One
, vol.10
, pp. e0130821
-
-
Marçais, G.1
Yorke, J.A.2
Zimin, A.3
-
21
-
-
84911413468
-
Trowel: A fast and accurate error correction module for Illumina sequencing reads
-
Lim, E.-C. et al. Trowel: a fast and accurate error correction module for Illumina sequencing reads. Bioinformatics 30, 3264-5 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 3264-3265
-
-
Lim, E.-C.1
-
22
-
-
78349249371
-
EDAR: An efficient error detection and removal algorithm for next generation sequencing data
-
Zhao, X. et al. EDAR: an efficient error detection and removal algorithm for next generation sequencing data. J. Comput. Biol. 17, 1549-60 (2010).
-
(2010)
J. Comput. Biol.
, vol.17
, pp. 1549-1560
-
-
Zhao, X.1
-
23
-
-
84929620856
-
Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data
-
Kimura, K. & Koike, A. Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data. Bioinformatics 31, 1577-83 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 1577-1583
-
-
Kimura, K.1
Koike, A.2
-
25
-
-
84867331947
-
A high-coverage genome sequence from an archaic Denisovan individual
-
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222-6 (2012).
-
(2012)
Science
, vol.338
, pp. 222-226
-
-
Meyer, M.1
-
26
-
-
84976897928
-
Database resources of the National Center for Biotechnology Information
-
NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 44, D7-19 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D7-19
-
-
-
27
-
-
0032876978
-
DbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation
-
Sherry, S. T., Ward, M. & Sirotkin, K. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 9, 677-9 (1999).
-
(1999)
Genome Res.
, vol.9
, pp. 677-679
-
-
Sherry, S.T.1
Ward, M.2
Sirotkin, K.3
-
28
-
-
84991529125
-
GenomeTester4: A toolkit for performing basic set operations-union, intersection and complement on k-mer lists
-
Kaplinski, L., Lepamets, M. & Remm, M. GenomeTester4: a toolkit for performing basic set operations-union, intersection and complement on k-mer lists. Gigascience 4, 58 (2015).
-
(2015)
Gigascience
, vol.4
, pp. 58
-
-
Kaplinski, L.1
Lepamets, M.2
Remm, M.3
-
29
-
-
84878234942
-
Characterizing and measuring bias in sequence data
-
Ross, M. G. et al. Characterizing and measuring bias in sequence data. Genome Biol. 14, R51 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R51
-
-
Ross, M.G.1
-
30
-
-
84960345468
-
Illumina error profiles: Resolving fine-scale variation in metagenomic sequencing data
-
Schirmer, M., D'Amore, R., Ijaz, U. Z., Hall, N. & Quince, C. Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics 17, 125 (2016).
-
(2016)
BMC Bioinformatics
, vol.17
, pp. 125
-
-
Schirmer, M.1
D'Amore, R.2
Ijaz, U.Z.3
Hall, N.4
Quince, C.5
-
31
-
-
79952592810
-
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
-
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764-770 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 764-770
-
-
Marçais, G.1
Kingsford, C.2
-
32
-
-
84929626489
-
KMC 2: Fast and resource-frugal k-mer counting
-
Deorowicz, S., Kokot, M., Grabowski, S. & Debudaj-Grabysz, A. KMC 2: Fast and resource-frugal k-mer counting. Bioinformatics 31, 1569-1576 (2014).
-
(2014)
Bioinformatics
, vol.31
, pp. 1569-1576
-
-
Deorowicz, S.1
Kokot, M.2
Grabowski, S.3
Debudaj-Grabysz, A.4
-
33
-
-
84874741072
-
DSK: K-mer counting with very low memory usage
-
Rizk, G., Lavenier, D. & Chikhi, R. DSK: K-mer counting with very low memory usage. Bioinformatics 29, 652-653 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 652-653
-
-
Rizk, G.1
Lavenier, D.2
Chikhi, R.3
-
34
-
-
84904013350
-
Turtle: Identifying frequent k-mers with cache-efficient algorithms
-
Roy, R. S., Bhattacharya, D. & Schliep, A. Turtle: Identifying frequent k-mers with cache-efficient algorithms. Bioinformatics 30, 1950-1957 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1950-1957
-
-
Roy, R.S.1
Bhattacharya, D.2
Schliep, A.3
-
35
-
-
81555208922
-
RNA-Seq and find: Entering the RNA deep field
-
Roberts, A. & Pachter, L. RNA-Seq and find: entering the RNA deep field. Genome Med 3, 74 (2011).
-
(2011)
Genome Med
, vol.3
, pp. 74
-
-
Roberts, A.1
Pachter, L.2
-
36
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
|