Literature DB >> 21208982

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

Heng Li1.   

Abstract

UNLABELLED: 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.

Mesh：

Year:  2011        PMID： 21208982      PMCID： PMC3042176          DOI： 10.1093/bioinformatics/btq671

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

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3.  Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.

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4.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

5.  BigWig and BigBed: enabling browsing of large distributed datasets.

Authors:  W J Kent; A S Zweig; G Barber; A S Hinrichs; D Karolchik
Journal:  Bioinformatics       Date:  2010-07-17       Impact factor: 6.937

6.  The UCSC Genome Browser database: update 2010.

Authors:  Brooke Rhead; Donna Karolchik; Robert M Kuhn; Angie S Hinrichs; Ann S Zweig; Pauline A Fujita; Mark Diekhans; Kayla E Smith; Kate R Rosenbloom; Brian J Raney; Andy Pohl; Michael Pheasant; Laurence R Meyer; Katrina Learned; Fan Hsu; Jennifer Hillman-Jackson; Rachel A Harte; Belinda Giardine; Timothy R Dreszer; Hiram Clawson; Galt P Barber; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971

7.  Accurate whole human genome sequencing using reversible terminator chemistry.

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Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962
  7 in total
  207 in total

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Journal:  Plant Physiol       Date:  2013-03-22       Impact factor: 8.340
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