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Volumn 6, Issue 11, 2017, Pages

Indexcov: Fast coverage quality control for whole-genome sequencing

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME ABERRATION; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE SEQUENCE; GENETIC VARIATION; HUMAN; INDEXCOV SOFTWARE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; QUALITY CONTROL; SEQUENCE ALIGNMENT; SOFTWARE; WHOLE GENOME SEQUENCING; HUMAN GENOME; PROCEDURES; REPRODUCIBILITY; STANDARDS;

EID: 85042178669     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1093/gigascience/gix090     Document Type: Article
Times cited : (34)

References (19)
  • 1
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li H, Handsaker B, Wysoker A et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25:2078-9.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 2
    • 85042185687 scopus 로고    scopus 로고
    • Accessed 27 May 2017
    • Samtools. https://samtools.github.io/hts-specs/CRAMv3.pdf. Accessed 27 May 2017.
  • 3
    • 84879043343 scopus 로고    scopus 로고
    • Quantifying single nucleotide variant detection sensitivity in exome sequencing
    • Meynert AM, Bicknell LS, Hurles ME et al. Quantifying single nucleotide variant detection sensitivity in exome sequencing. BMC Bioinformatics 2013;14:195.
    • (2013) BMC Bioinformatics , vol.14 , pp. 195
    • Meynert, A.M.1    Bicknell, L.S.2    Hurles, M.E.3
  • 4
    • 84912096454 scopus 로고    scopus 로고
    • LUMPY: a probabilistic framework for structural variant discovery
    • Layer RM, Chiang C, Quinlan AR et al. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol 2014;15:R84.
    • (2014) Genome Biol , vol.15 , pp. R84
    • Layer, R.M.1    Chiang, C.2    Quinlan, A.R.3
  • 5
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping
    • Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet 2011;12: 363-76.
    • (2011) Nat Rev Genet , vol.12 , pp. 363-376
    • Alkan, C.1    Coe, B.P.2    Eichler, E.E.3
  • 6
    • 84927151856 scopus 로고    scopus 로고
    • bam.iobio: a web-based, real-time, sequence alignment file inspector
    • Miller CA, Qiao Y, Disera T et al. bam.iobio: a web-based, real-time, sequence alignment file inspector. Nat Methods 2014;11:1189.
    • (2014) Nat Methods , vol.11 , pp. 1189
    • Miller, C.A.1    Qiao, Y.2    Disera, T.3
  • 7
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010;26: 841-2.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 8
    • 77956873627 scopus 로고    scopus 로고
    • Tackling the widespread and critical impact of batch effects in high-throughput data
    • Leek JT, Scharpf RB, Bravo HC et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet 2010;11:733-9.
    • (2010) Nat Rev Genet , vol.11 , pp. 733-739
    • Leek, J.T.1    Scharpf, R.B.2    Bravo, H.C.3
  • 9
    • 85042184551 scopus 로고    scopus 로고
    • bíogo/hts: high throughput sequence handling for the Go language
    • Kortschak RD, Pedersen BS, Adelson DL. bíogo/hts: high throughput sequence handling for the Go language. J Open Source Softw 2017. http://dx.doi.org/10.21105/joss.00168.
    • (2017) J Open Source Softw
    • Kortschak, R.D.1    Pedersen, B.S.2    Adelson, D.L.3
  • 10
    • 85042199758 scopus 로고    scopus 로고
    • Accessed August 2017
    • ftp://ftp.sra.ebi.ac.uk/vol1/ERA172/ERA172924/bam/NA1287 8 S1.bam. Accessed August 2017.
  • 11
    • 84913546864 scopus 로고    scopus 로고
    • 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 2014;30:2843-51.
    • (2014) Bioinformatics , vol.30 , pp. 2843-2851
    • Li, H.1
  • 12
    • 84861548193 scopus 로고    scopus 로고
    • Summarizing and correcting the GC content bias in high-throughput sequencing
    • Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 2012;40:e72.
    • (2012) Nucleic Acids Res , vol.40
    • Benjamini, Y.1    Speed, T.P.2
  • 13
    • 85047966472 scopus 로고    scopus 로고
    • Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2076 genomes in quartet families
    • Werling DM. Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2076 genomes in quartet families. bioRxiv 2017;127043. doi:10.1101/127043.
    • (2017) bioRxiv , pp. 127043
    • Werling, D.M.1
  • 14
    • 84867076609 scopus 로고    scopus 로고
    • Dosage effects of X and Y chromosomes on language and social functioning in children with supernumerary sex chromosome aneuploidies: implications for idiopathic language impairment and autism spectrum disorders
    • Lee NR, Wallace GL, Adeyemi EI et al. Dosage effects of X and Y chromosomes on language and social functioning in children with supernumerary sex chromosome aneuploidies: implications for idiopathic language impairment and autism spectrum disorders. J Child Psychol Psychiatry 2012;53:1072-81.
    • (2012) J Child Psychol Psychiatry , vol.53 , pp. 1072-1081
    • Lee, N.R.1    Wallace, G.L.2    Adeyemi, E.I.3
  • 15
    • 84942113437 scopus 로고    scopus 로고
    • Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci
    • Sanders SJ, He X, Willsey AJ et al. Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron 2015;87:1215-33.
    • (2015) Neuron , vol.87 , pp. 1215-1233
    • Sanders, S.J.1    He, X.2    Willsey, A.J.3
  • 16
    • 79951993896 scopus 로고    scopus 로고
    • Tabix: fast retrieval of sequence features from generic TAB-delimited files
    • Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics 2011;27: 718-9.
    • (2011) Bioinformatics , vol.27 , pp. 718-719
    • Li, H.1
  • 17
    • 85042201930 scopus 로고    scopus 로고
    • Accessed August 2017
    • Brent S Pedersen. http://bit.ly/indexcov-example, Accessed August 2017.
  • 18
    • 85042188306 scopus 로고    scopus 로고
    • Accessed August 2017
    • Brent S Pedersen. https://github.com/brentp/goleft. Accessed August 2017.
  • 19
    • 85042177707 scopus 로고    scopus 로고
    • Supporting software for "Indexcov: fast coverage quality control for whole-genome sequencing"
    • Pedersen BS, Collins RL, Talkowski ME et al. Supporting software for "Indexcov: fast coverage quality control for whole-genome sequencing." GigaScience Database. 2017. http://dx.doi.org/10.5524/100349.
    • (2017) GigaScience Database
    • Pedersen, B.S.1    Collins, R.L.2    Talkowski, M.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.