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extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output
C
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Makefile
README
endian.h
main.c
sff.c
sff.h

README

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.

Below is the help message (via 'sff2fastq -h') describing its usage.

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.

AUTHOR
======

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

ACKNOWLEDGEMENTS
================

This software was developed at The Genome Center 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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