Difference between revisions of "Maq"

Latest revision as of 19:47, 12 August 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 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|maq}}
@@ 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_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_MAQ_BIN - executable directory
 <!--Additional-->