Maq

Maq^[1] joins the Sequencher family of plugins in version 5.0. The popular Maq algorithm can align single-end and paired- end next-generation data to a reference sequence. It was originally designed to align Illumina-Solexa data but will, in fact, align any very short read data (63 bases or less). The reference sequence may be in the form of a FastA or GenBank file.  Maq uses binary formats to compress the reference and reads files. Best of all, Maq requires very little RAM to run which makes it even easier to perform next-generation sequencing using your desktop computer.

Maq was written to run on the command line. Sequencher provides an straightforward, easy to use interface which protects you from the command line and from having to learn use command line arguments.

Save your results in Maq’s own format or SAM format, so you may view the results of your alignments in Maqview or Tablet.