Difference between revisions of "Maq"

Latest revision as of 19:47, 12 August 2022

Description

maq website

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.

Documentation:

Environment Modules

Run module spider maq to find out what environment modules are available for this application.

System Variables

HPC_MAQ_DIR - installation directory
HPC_MAQ_BIN - executable directory

Additional Information

From the Maq website:

Follow these steps to run Maq. All you need is a reference sequence file in the FASTA format.

Prepare a reference sequence (ref.fasta), better a bacterial genome to make the test run faster.

Simulate diploid reference and read sequences, map reads, call variants and evaluate the results in one go:

maq.pl demo ref.fasta calib-30.dat

where calib-30.dat is contained in maq-data.

View the alignment:

cd maqdemo/easyrun;
maqindex -i -c consensus.cns all.map;
maqview -c consensus.cns all.map

Even for advanced maq users, running `maq.pl demo' is recommended. You may find something helpful.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|maq}}
 |{{#vardefine:url|http://maq.sourceforge.net/}}
 <!--CONFIGURATION: OPTIONAL (1=ON)-->
-|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
-|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
-|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 |{{#vardefine:exe|1}} <!--RUNNING -->
 |{{#vardefine:conf|}} <!--CONFIGS-->
@@ Line 27: / Line 24: @@
 * [http://maq.sourceforge.net/maq-manpage.shtml Maq Reference Manual]
 * [http://maq.sourceforge.net/faq.shtml Maq FAQ]
 <!--Modules-->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+==Environment Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_MAQ_BIN - executable directory
-<!--Run-->
+<!--Additional-->
-{{#if: {{#var: exe}}|==How To Run==
+{{#if: {{#var: exe}}|==Additional Information==
 From the Maq website:
@@ Line 63: / Line 59: @@
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 <!--Policy-->
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 |}}