You are here

GMAP (with GSNAP) - Genomic mapping and alignment

Table of Contents

Introduction

From the GMAP web site, GMAP is described as a genomic mapping and alignment program for mRNA and EST sequences.  An accompanying program, GSNAP, is a short-read nucleotide alignment program.

The software has been installed on Bugaboo and Breezy.  See the software versions page (also available through a tab above).

Running GMAP and GSNAP on Bugaboo

The binaries for the programs in the GMAP package (version of 2014-10-22) are on the default path on Bugaboo.

Running GMAP and GSNAP on Breezy

The binaries for the programs in the GMAP package (version of 2014-10-22) are located in /global/software/gmap/gmap_20141022/bin.

The main documentation for the program appears to be the README file that accompanies the distribution.  This is available at /global/software/gmap/gmap_20141022/README .

Please read the README file, in particular the section on multi-threaded processing before running the program.

For More Information

2014-11-23 - Documenting installation of the 2014-10-22 release of the GMAP package.