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

Heng Li | Zendy

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

Author(s) -

Heng Li

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btq671

Subject(s) - perl , computer science , python (programming language) , file transfer protocol , sql , java , file format , software , ascii , world wide web , information retrieval , database , operating system , the internet

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.

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