SAMtools.FastaIndex (v2)

Indexes a reference sequence in FASTA format

Author: Marc-Danie Nazaire,, Broad Institute


Algorithm Version: 0.1.19


This module indexes a reference sequence in FASTA format. The index file is given the extension FAI.

This module wraps the faidx function of SAMtools.
For more information on FASTA format, see a description of it here:
and also here:


Name Description
fasta file * A sequence in FASTA format.
output prefix * The prefix to use for the output file name

* - required

Input Files

  1. fasta.file
    A sequence in FASTA format. (gz compressed files are supported)

Output Files

  1. FAI file
    An index of a FASTA sequence file.
  2. FASTA file
    A copy of the FASTA input file.


Requires Macintosh or Linux OS.

Platform Dependencies

Task Type:
Preprocess & Utilities

CPU Type:

Operating System:


Version Comments

Version Release Date Description
2 2014-08-20 Converted doc to html, modified to install SAMtools using plugin mechanism, and fixed bug with using external url
1 2011-07-08