Introduction
Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available at http://sourceforge.net/projects/maq/. Maq is previously known as mapass2.
Run Maq Now
Follow these steps to try Maq. All you need is a reference sequence file in the FASTA format.
- Prepare a reference sequence (ref.fasta). Better a bacterial genome.
- Download maq, maq-data and maqview at the download page.
- Copy maq, maq.pl and maq_eval.pl to the $PATH or to the same directory.
- 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.
Documentations
Maq is documented in three parts: Maq User's Manual, Maq Reference Manual and FAQ page. The user's manual introduces basic functions in maq, the reference manual gives detailed usage of each function and wiki site presents informal but useful tips and notes related to maq. These documentations are complementary to each other.
News
- Maq 0.6.6 Released (Release Notes) - 2008.04.27
- Maq 0.6.5 Released (Release Notes) - 2008.03.28
- Maqview 0.2.3 Released (Release Notes) - 2008.01.03
- Maq 0.6.4 Released (Release Notes) - 2008.04.27
- Maqview 0.2.1 Released (Release Notes) - 2008.01.03
- Maq 0.6.3 Released (Release Notes) - 2008.01.03
- Maq 0.6.1 Released (Release Notes) - 2007.10.03
- Maqview 0.1.1 Released (Release Notes) - 2007.09.27
- Maqview 0.1.0 Released (Release Notes) - 2007.09.24
- Maq 0.6.0 Released (Release Notes) - 2007.09.05
- Maq 0.5.1 Released (Release Notes) - 2007.07.31
- tgap-maq 20070715 Released - 2007.07.15
- Maq 0.5.0 Released (Release Notes) - 2007.07.15
- Mapass2 is now formally renamed as maq, which stands for Mapping and Assembly with Quality. - 2007.07.15
- Mapass2 0.4.3 Released (Release Notes) - 2007.07.04
- Bug fix in the easyrun script mapass2.pl. The earlier version of this script failed to give correct results when several read files are given. Please download the latest version version from this website. I am sorry for the inconvenience this bug may bring. This fix will be incorporated in the next release.
- Mapass2 0.4.2 Released (Release Notes) - 2007.06.21
- Mapass2 0.4.1 Released (Release Notes) - 2007.06.17
- Mapass2 0.4.0 Released (Release Notes) - 2007.05.15
- Mapass Help Mailing List Opened - 2007.05.11
- Mapass2 0.3.1 Released (Release Notes) - 2007.05.09
- Mapass2 0.3.0 Released (Release Notes) - 2007.05.03
- Mapass2 0.2.1 Released (Release Notes) - 2007.04.23
- Mapass2 0.2.0 Released (Release Notes) - 2007.04.22
- Mapass Announcement Mailing List Opened - 2007.04.16
- Mapass Registered at SourceForge.net - 2007.03.21