Difference between revisions of "Maq"

Revision as of 18:31, 10 June 2022

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

Documentation:

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

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 25: / Line 25: @@
 * [http://maq.sourceforge.net/faq.shtml Maq FAQ]
 <!--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==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
@@ Line 80: / Line 78: @@
 See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 __NOTOC____NOEDITSECTION__
-=Validation=
-* Validated 4/5/2018