Difference between revisions of "Maq"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
Line 25: Line 25:
 
* [http://maq.sourceforge.net/faq.shtml Maq FAQ]
 
* [http://maq.sourceforge.net/faq.shtml Maq FAQ]
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
[[Modules|modules documentation]]
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*{{#var:app}}
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
Line 80: Line 78:
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validated 4/5/2018
 

Revision as of 18:31, 10 June 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.