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

• Published in: Bioinformatics (Oxford, England) Vol. 27; no. 5; pp. 718 - 719
• Main Author: Li, Heng
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.03.2011
• Subjects: Algorithms; Applications Note; Biological and medical sciences; Computational Biology - methods; Fundamental and applied biological sciences. Psychology; General aspects; Genome; Genomics - methods; Information Storage and Retrieval - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Sequence Analysis, DNA - methods; Software; File
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/btq671

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. Contact:  hengli@broadinstitute.org