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. 2011 Mar 1;27(5):718-9.
doi: 10.1093/bioinformatics/btq671. Epub 2011 Jan 5.

Tabix: fast retrieval of sequence features from generic TAB-delimited files

Heng Li  1
Affiliations

Tabix: fast retrieval of sequence features from generic TAB-delimited files

Heng Li. Bioinformatics. .

Abstract

Tabix is the first generic tool that indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves features overlapping specified regions. Tabix features include few seek function calls per query, data compression with gzip compatibility and direct FTP/HTTP access. Tabix is implemented as a free command-line tool as well as a library in C, Java, Perl and Python. It is particularly useful for manually examining local genomic features on the command line and enables genome viewers to support huge data files and remote custom tracks over networks.

Availability and implementation: http://samtools.sourceforge.net.

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References

    1. Alekseyenko AV, Lee CJ. Nested containment list (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics. 2007;23:1386–1393. - PubMed
    1. Bentley DR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456:53–59. - PMC - PubMed
    1. Kent WJ, et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. - PMC - PubMed
    1. Kent WJ, et al. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010;26:2204–2207. - PMC - PubMed
    1. Li H, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–2079. - PMC - PubMed

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