Maq stands for Mapping and Assembly with Quality. It builds assembly by mapping short reads to reference sequences. Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.
Maq first aligns reads to reference sequences and then calls the consensus. At the mapping stage, maq performs ungapped alignment. For single-end reads, maq is able to find all hits with up to 2 or 3 mismatches, depending on a command-line option; for paired-end reads, it always finds all paired hits with one of the two reads containing up to 1 mismatch. At the assembling stage, maq calls the consensus based on a statistical model. It calls the base which maximizes the posterior probability and calculates a phred quality at each position along the consensus. Heterozygotes are also called in this process.
Maq is a project hosted by SourceForge.net. The project page is available at http://sourceforge.net/projects/maq/.
Version
Type '/usr/local/maq/bin/maq.pl' on commend line.
Sample Session on Biowulf
DO NOT RUN MAQ ON BIOWULF HEAD NODE. MAQ sample files can be copied from:
/usr/local/maq/ref.fasta and /usr/local/maq/calib-36.dat.gz.
Submitting a single MAQ batch job
1. Create a script file. The file content will be similar to below:
# This file name is runMAQ
#
#PBS -N MAQ
#PBS -m be
#PBS -k oe
cd /home/user/maq/run1
/usr/local/maq/maq-0.7.1/bin/maq.pl demo ref.fasta calib-36.dat
2. submit the script using the 'qsub' command, e.g.
qsub -l nodes=1:x86-64:m8192 /home/username/runMAQ
Submitting a swarm of MAQ jobs
Using the 'swarm' utility, one can submit many jobs to the cluster to run spontaneously.
Set up a swarm command file (eg /home/username/cmdfile). Here is a sample file:
/usr/local/maq/maq-0.7.1/bin/maq.pl demo ref2.fasta calib-2.dat
/usr/local/maq/maq-0.7.1/bin/maq.pl demo ref3.fasta calib-3.dat
....
/usr/local/maq/maq-0.7.1/bin/maq.pl demo refN.fasta calib-n.dat
Each line of the commands above will be executed on one processor.
Submit this swarm command file to the batch system with the command:
biowulf> % swarm -f comdfile -l nodes=1:m8192:x86-64
Swarm utility program will create the batch scripts and submit them to the batch system.
Note, if your job requires more than 8gb of memory, request g72 instead of m8192 and change the 'n' number based on your requirement. For example, if your job require 24 gb of memory each:
g72 nodes have 72 gb of memory each.
Documentation
http://maq.sourceforge.net/index.shtml
