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

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Zeitschriftentitel: Bioinformatics
Personen und Körperschaften: Li, Heng
In: Bioinformatics, 27, 2011, 5, S. 718-719
Format: E-Article
Sprache: Englisch
veröffentlicht:
Oxford University Press (OUP)
Schlagwörter:
Computational Mathematics
Computational Theory and Mathematics
Computer Science Applications
Molecular Biology
Biochemistry
Statistics and Probability
author_facet Li, Heng
Li, Heng
author Li, Heng
spellingShingle Li, Heng
Bioinformatics
Tabix: fast retrieval of sequence features from generic TAB-delimited files
Computational Mathematics
Computational Theory and Mathematics
Computer Science Applications
Molecular Biology
Biochemistry
Statistics and Probability
author_sort li, heng
spelling Li, Heng 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btq671 <jats:title>Abstract</jats:title> <jats:p>Summary: 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.</jats:p> <jats:p>Availability and Implementation: http://samtools.sourceforge.net.</jats:p> <jats:p>Contact: hengli@broadinstitute.org</jats:p> Tabix: fast retrieval of sequence features from generic TAB-delimited files Bioinformatics
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title Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_unstemmed Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_full Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_fullStr Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_full_unstemmed Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_short Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_sort tabix: fast retrieval of sequence features from generic tab-delimited files
topic Computational Mathematics
Computational Theory and Mathematics
Computer Science Applications
Molecular Biology
Biochemistry
Statistics and Probability
url http://dx.doi.org/10.1093/bioinformatics/btq671
publishDate 2011
physical 718-719
description <jats:title>Abstract</jats:title> <jats:p>Summary: 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.</jats:p> <jats:p>Availability and Implementation:  http://samtools.sourceforge.net.</jats:p> <jats:p>Contact:  hengli@broadinstitute.org</jats:p>
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description <jats:title>Abstract</jats:title> <jats:p>Summary: 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.</jats:p> <jats:p>Availability and Implementation:  http://samtools.sourceforge.net.</jats:p> <jats:p>Contact:  hengli@broadinstitute.org</jats:p>
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spelling Li, Heng 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btq671 <jats:title>Abstract</jats:title> <jats:p>Summary: 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.</jats:p> <jats:p>Availability and Implementation: http://samtools.sourceforge.net.</jats:p> <jats:p>Contact: hengli@broadinstitute.org</jats:p> Tabix: fast retrieval of sequence features from generic TAB-delimited files Bioinformatics
spellingShingle Li, Heng, Bioinformatics, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability
title Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_full Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_fullStr Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_full_unstemmed Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_short Tabix: fast retrieval of sequence features from generic TAB-delimited files
title_sort tabix: fast retrieval of sequence features from generic tab-delimited files
title_unstemmed Tabix: fast retrieval of sequence features from generic TAB-delimited files
topic Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability
url http://dx.doi.org/10.1093/bioinformatics/btq671