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extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output

branch: master

+ update the version to 0.9.0

  - these reflect the changes to handle:
     * stdin input
     * handle zero length reads
       (may occur after trimming and/or de-multiplexing)
latest commit 4945f3b578
Indraniel authored
Octocat-spinner-32 Makefile + Makefile correction March 24, 2010
Octocat-spinner-32 README.md + update contributor list November 11, 2013
Octocat-spinner-32 endian.h + addition of genome center linux image alterations October 04, 2009
Octocat-spinner-32 main.c + update the version to 0.9.0 November 11, 2013
Octocat-spinner-32 sff.c handle reads that are completely trimmed, eg after demultiplex May 11, 2012
Octocat-spinner-32 sff.h + refactoring: movement of sff specific functions from main.c to sff.c March 25, 2010
README.md

SYNOPSIS

The program sff2fastq extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.

USAGE

Given an SFF file, file.sff you can simply run:

sff2fastq file.sff

sff2fastq will also read from standard input if a SFF file is not specified on the command line. For example, you can do the following:

cat file.sff | sff2fastq > file.fastq

This is useful if you have a compressed sff file and you'd like to avoid creating temporary files like so:

zcat file.sff.gz | sff2fastq > file.fastq

(This feature has been kindly added by Björn Winckler )

Options

Below is the help message (via sff2fastq -h) describing its usage & options:

Usage: sff2fastq [options] [sff_file]
        -h                  This help message   
        -v                  Program and version information
        -n                  Output the untrimmed sequence
        -o <fastq_file>     Desired fastq output file. If not specified, 
                            defaults to stdout

INSTALLATION

The installation process currently consists of a very simple Makefile.

Just do the following:

git clone git://github.com/indraniel/sff2fastq.git;
cd sff2fastq;
make; # try 'make genome' if at the Genome Center at Washington University
      # or on a Linux distribution from 2008 or earlier

The sff2fastq executable should be in the working directory. Afterwards, you can move the executable to wherever you wish.

NOTES

This has been successfully compiled on Linux/Ubuntu 8.04 & 9.10 workstations (both 32-bit and 64-bit machines), and on Mac OS X (version 10.5). Compiling on other types of operating systems and architectures has not been experimented upon.

The FASTQ output produced is of the Sanger FASTQ format as described here (http://maq.sourceforge.net/fastq.shtml).

Without any given options the default approach is to output trimmed sequence and quality values. This is similar in nature to the sff tools produced by 454 Life Sciences/Roche.

AUTHORS

Indraniel Das (indraniel@gmail.com or idas@wustl.edu) The Genome Institute at Washington University

Contributors

ACKNOWLEDGEMENTS

This software was developed at The Genome Institute at Washington University, St. Louis, MO.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

March 23, 2010

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