Difference between revisions of "Maq"

Revision as of 19:03, 10 August 2012

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

Documentation:

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 4: / Line 4: @@
 |{{#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-->
 ==Required Modules==
@@ Line 34: / Line 29: @@
 ===Serial===
 *{{#var:app}}
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
-* HPC_MAQ_BIN - executable directory
 ==System Variables==
 * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
-<!--Run-->
+* HPC_MAQ_BIN - executable directory
+<!--Additional-->
-{{#if: {{#var: exe}}|==How To Run==
+{{#if: {{#var: exe}}|==Additional Information==
 From the Maq website: