Best of all, Maq requires very little RAM to run which makes it even easier to perform next-generation sequencing. Maq uses binary formats to compress the reference and reads files. The reference sequence may be in the form of a FastA or GenBank file. Originally designed to align Illumina-Solexa data, it will align any very short read data (63 bases or less). The popular Maq algorithm aligns single-end and paired-end Next-Generation data to a reference sequence.
Maq (3)joined the Sequencher family of plugins in version 5.0. The results of any alignment with GSNAP can be viewed in the popular Tablet browser.įor the power users amongst you who want greater control of GSNAP’s command line functions, press Advanced (Edit) to open the Advanced GSNAP Options dialogue where you may configure specific command line arguments. Sequencher automatically divides the data by barcode into separate files, aligns these to the reference using GSNAP, and places the results into separate results folders. Now you have Sequencher’s user-friendly interface which allows you to harness GSNAP’s power with your MID data. GSNAP can now work with Multiplex ID (MID) data thereby maximizing efficiency even further. Length of the sequence is not an issue with GSNAP because it has the ability to align very short to arbitrarily long data lengths with ease. GSNAP is designed to preform reference-based alignment of Illumina-Solexa or Sanger standard data that is both paired-ended and unpaired-ended. This allows GSNAP to be faster and easier while performing Next-Gen sequencing. GSNAP uses highly efficient methods for reference- based alignment by compressing the reference sequence.
GSNAP (2) joined the Sequencher family of plugins in version 5.0. For the power users amongst you who want access to those command line functions,the Advanced (Edit) dialog lets you harness those too. Sequencher provides you with an easy to use interface that insulates you from the command line and from having to learn or use command line arguments. BWA was written to run on the command line.
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