Maq

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:
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年04月27日
Maq 0.6.5 Released (Release Notes) - 2008年03月28日
Maqview 0.2.3 Released (Release Notes) - 2008年01月03日
Maq 0.6.4 Released (Release Notes) - 2008年04月27日
Maqview 0.2.1 Released (Release Notes) - 2008年01月03日
Maq 0.6.3 Released (Release Notes) - 2008年01月03日
Maq 0.6.1 Released (Release Notes) - 2007年10月03日
Maqview 0.1.1 Released (Release Notes) - 2007年09月27日
Maqview 0.1.0 Released (Release Notes) - 2007年09月24日
Maq 0.6.0 Released (Release Notes) - 2007年09月05日
Maq 0.5.1 Released (Release Notes) - 2007年07月31日
tgap-maq 20070715 Released - 2007年07月15日
Maq 0.5.0 Released (Release Notes) - 2007年07月15日
Mapass2 is now formally renamed as maq, which stands for Mapping and Assembly with Quality. - 2007年07月15日
Mapass2 0.4.3 Released (Release Notes) - 2007年07月04日
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年06月21日
Mapass2 0.4.1 Released (Release Notes) - 2007年06月17日
Mapass2 0.4.0 Released (Release Notes) - 2007年05月15日
Mapass Help Mailing List Opened - 2007年05月11日
Mapass2 0.3.1 Released (Release Notes) - 2007年05月09日
Mapass2 0.3.0 Released (Release Notes) - 2007年05月03日
Mapass2 0.2.1 Released (Release Notes) - 2007年04月23日
Mapass2 0.2.0 Released (Release Notes) - 2007年04月22日
Mapass Announcement Mailing List Opened - 2007年04月16日
Mapass Registered at SourceForge.net - 2007年03月21日