forked from indraniel/sff2fastq
-
Notifications
You must be signed in to change notification settings - Fork 0
lh3/sff2fastq
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
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
About
extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output
Resources
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published