-
1
-
-
10244239321
-
Life with 6000 genes
-
Goffeau A., et al. Life with 6000 genes. Science 1996, 274:546-567.
-
(1996)
Science
, vol.274
, pp. 546-567
-
-
Goffeau, A.1
-
2
-
-
84865591846
-
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
-
Quail M.A., et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012, 13:341.
-
(2012)
BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.A.1
-
3
-
-
84880715396
-
Advantages of single-molecule real-time sequencing in high-GC content genomes
-
Shin S.C., et al. Advantages of single-molecule real-time sequencing in high-GC content genomes. PLoS ONE 2013, 8:e68824.
-
(2013)
PLoS ONE
, vol.8
-
-
Shin, S.C.1
-
4
-
-
84855219212
-
Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes
-
Oyola S.O., et al. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 2012, 13:1.
-
(2012)
BMC Genomics
, vol.13
, pp. 1
-
-
Oyola, S.O.1
-
5
-
-
84880798154
-
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
-
Chin C-S., et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 2013, 10:563-569.
-
(2013)
Nat. Methods
, vol.10
, pp. 563-569
-
-
Chin, C.-S.1
-
6
-
-
84865992574
-
A survey of error-correction methods for next-generation sequencing
-
Yang X., et al. A survey of error-correction methods for next-generation sequencing. Brief. Bioinform. 2013, 14:56-66.
-
(2013)
Brief. Bioinform.
, vol.14
, pp. 56-66
-
-
Yang, X.1
-
7
-
-
84857838310
-
Efficient de novo assembly of large genomes using compressed data structures
-
Simpson J.T., Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 2012, 22:549-556.
-
(2012)
Genome Res.
, vol.22
, pp. 549-556
-
-
Simpson, J.T.1
Durbin, R.2
-
8
-
-
70350669879
-
TagDust: a program to eliminate artifacts from next generation sequencing data
-
Lassmann T., et al. TagDust: a program to eliminate artifacts from next generation sequencing data. Bioinformatics 2009, 25:2839-2840.
-
(2009)
Bioinformatics
, vol.25
, pp. 2839-2840
-
-
Lassmann, T.1
-
9
-
-
83055181941
-
Assemblathon 1: a competitive assessment of de novo short read assembly methods
-
Earl D., et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011, 21:2224-2241.
-
(2011)
Genome Res.
, vol.21
, pp. 2224-2241
-
-
Earl, D.1
-
10
-
-
84991528460
-
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
-
Bradnam K.R., et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2013, 2:1-31.
-
(2013)
GigaScience
, vol.2
, pp. 1-31
-
-
Bradnam, K.R.1
-
11
-
-
79951530130
-
Scaffolding pre-assembled contigs using SSPACE
-
Boetzer M., et al. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011, 27:578-579.
-
(2011)
Bioinformatics
, vol.27
, pp. 578-579
-
-
Boetzer, M.1
-
12
-
-
84866391549
-
An integrated pipeline for de novo assembly of microbial genomes
-
Tritt A., et al. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 2012, 7:e42304.
-
(2012)
PLoS ONE
, vol.7
-
-
Tritt, A.1
-
13
-
-
77950658346
-
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
-
Tsai I.J., et al. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 2010, 11:R41.
-
(2010)
Genome Biol.
, vol.11
-
-
Tsai, I.J.1
-
14
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18:821.
-
(2008)
Genome Res.
, vol.18
, pp. 821
-
-
Zerbino, D.R.1
Birney, E.2
-
15
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren S., et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 2012, 30:692-697.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 692-697
-
-
Koren, S.1
-
16
-
-
84869814079
-
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology
-
English A.C., et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS ONE 2012, 7:e47768.
-
(2012)
PLoS ONE
, vol.7
-
-
English, A.C.1
-
17
-
-
0036673472
-
Automated de novo identification of repeat sequence families in sequenced genomes
-
Bao Z., Eddy S.R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002, 12:1269-1276.
-
(2002)
Genome Res.
, vol.12
, pp. 1269-1276
-
-
Bao, Z.1
Eddy, S.R.2
-
18
-
-
84899911097
-
-
1996-2004. RepeatMasker Open-3.0.
-
Smit, A. et al. (2006) 1996-2004. RepeatMasker Open-3.0. http://www.repeatmasker.org.
-
(2006)
-
-
Smit, A.1
-
19
-
-
84859898660
-
A beginner's guide to eukaryotic genome annotation
-
Yandell M., Ence D. A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet. 2012, 13:329-342.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 329-342
-
-
Yandell, M.1
Ence, D.2
-
20
-
-
24044447664
-
Automated generation of heuristics for biological sequence comparison
-
Slater G.S., Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 31
-
-
Slater, G.S.1
Birney, E.2
-
21
-
-
0036226603
-
BLAT: the BLAST-like alignment tool
-
Kent W.J. BLAT: the BLAST-like alignment tool. Genome Res. 2002, 12:656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
22
-
-
74049108922
-
BLAST+: architecture and applications
-
Camacho C., et al. BLAST+: architecture and applications. BMC Bioinformatics 2009, 10:421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
-
23
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C., et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28:511-515.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
-
24
-
-
40049091292
-
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
-
Stanke M., et al. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 2008, 24:637-644.
-
(2008)
Bioinformatics
, vol.24
, pp. 637-644
-
-
Stanke, M.1
-
25
-
-
2942544417
-
Gene finding in novel genomes
-
Korf I. Gene finding in novel genomes. BMC Bioinformatics 2004, 5:59.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 59
-
-
Korf, I.1
-
26
-
-
42949086676
-
Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments
-
Haas B.J., et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 2008, 9:R7.
-
(2008)
Genome Biol.
, vol.9
-
-
Haas, B.J.1
-
27
-
-
84859460610
-
Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing
-
de Jonge R., et al. Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:5110-5115.
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 5110-5115
-
-
de Jonge, R.1
-
28
-
-
84881145993
-
Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen
-
de Jonge R., et al. Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen. Genome Res. 2013, 23:1271-1282.
-
(2013)
Genome Res.
, vol.23
, pp. 1271-1282
-
-
de Jonge, R.1
-
29
-
-
84876266928
-
QUAST: quality assessment tool for genome assemblies
-
Gurevich A., et al. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013, 29:1072-1075.
-
(2013)
Bioinformatics
, vol.29
, pp. 1072-1075
-
-
Gurevich, A.1
-
30
-
-
46149104413
-
Mechanisms of intron gain and loss in Cryptococcus
-
Sharpton T.J., et al. Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 2008, 9:R24.
-
(2008)
Genome Biol.
, vol.9
-
-
Sharpton, T.J.1
|