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With Maq you can: - Fast align Illumina/SOLiD reads to the reference genome. With the default options, one million pairs of reads can be mapped to the human genome in about 10 CPU hours with less than 1G memory. - Accurately measure the error probability of the alignment of each individual read. - Call the consensus genotypes, including homozygous and heterozygous polymorphisms, with a Phred probabilistic quality assigned to each base. - Find short indels with paired end reads. - Accurately find large scale genomic deletions and translocations with paired end reads. - Discover potential CNVs by checking read depth. - Evaluate the accuracy of raw base qualities from sequencers and help to check the systematic errors.
However, Maq can NOT: - Do de novo assembly. (Maq can only call the consensus by mapping reads to a known reference.) - Map shorts reads against themselves. (Maq can only find complete overlap between reads.) - Align capillary reads or 454 reads to the reference. (Maq cannot align reads longer than 63bp.)
This package is likely to be useful for users working with genetics or genomic studies in biology who need to assembly DNA sequences from fixed-length sequencers.
Mapass2 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, which typically generates reads 25-35bp in length. Mapass2 first aligns reads to reference sequences and then calls the consensus. At the mapping stage, maq performs ungapped alignment. For single-end rea more»
Beta Release 0.7.1 (26 September, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Version 0.7.0 does not work with reads >63bp at all. I overlooked two lines of codes which assume reads are 63bp or shorter. Now I have fixed the bug and tested it on simulated long reads. It seems to work fine. I am sorry for this obvious bug. No other things are changed since 0.7.0. (0.7.1: 26 September 2008, r672) more»
MAQ(1) Bioinformatics Tools MAQ(1) NAME Maq - Mapping and Assembly with Qualities SYNOPSIS maq command [options] arguments maq.pl command [options] arguments DESCRIPTION Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed more»
maq (0.7.1-3) unstable; urgency=low * Distribute scripts that are not installed by upstream’s more»
------------------------------------------------------------------------ r666 | lh3lh3 | 2008-09-21 more»
Heng Li wrote all the codes of this project.