Difference between revisions of "MUMmer"

Revision as of 19:19, 10 August 2012

Description

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

Required Modules

modules documentation

Serial

mummer

System Variables

HPC_{{#uppercase:mummer}}_DIR - installation directory

@@ Line 20: / Line 20: @@
 MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
 <!--Modules-->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+==Required Modules==
+[[Modules|modules documentation]]
-To use {{#var:app}} with the environment modules system at HPC the following commands are available:
+===Serial===
+*{{#var:app}}
-Get module information for {{lc: {{PAGENAME}}}}:
+==System Variables==
- $module spider {{#var:app}}
+* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
-{{#if: {{#var:intel}}|Load Intel compiler: {{#tag:pre|$module load intel/{{#var:intel}}}}|}}{{#if: {{#var:mpi}}|Load MPI implementation: {{#tag:pre|$module load {{#var:mpi}}}}|}}
-Load the perl module:
- $module load perl
-Load the application module:
- $module load {{#var:app}}
-or in one command:
- $module load perl mummer
-The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
-* HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.|}}
-* HPC_MUMMER_BIN - executable directory
 {{#if: {{#var: exe}}|==How To Run==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}