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samtools faidx

By Li H., Durbin R., Last update 1494698999
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samtools faidx description

Samtools faidx indexes reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create .fai on the disk. If regions are speficified, the subsequences will be retrieved and printed to stdout in the FASTA format. The input file can be compressed in the RAZF format


Parent program: samtools

SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. It is very convinient for handling reads mapped to reference genome. Normally SAMtools is used in intermediate step between raw read mapping and SNP or variants callingm, because it allows to effeciently store mapped reads.