GSNAP

GSNAP^[1] joins the Sequencher family of plugins in version 5.0. GSNAP can align Illumina-Solexa or Sanger standard FastQ data. It is designed to deal with data from very short (14 bases) to arbitrarily long data. GSNAP can align single-end, and paired-end next-generation data to a reference sequence. The reference sequence may be in the form of a FastA or GenBank file. GSNAP uses highly efficient methods for compressing the reference sequence and thereby speeding up the program. Such an efficient use of resources makes it even easier to perform Next Gen sequencing using your desktop computer.

GSNAP was written to run on the command line. Sequencher provides you with an easy to use interface which protects you from the command line and from having to learn or use command line arguments.

The results of the alignment are saved in SAM format so you can use the popular Tablet browser to view your alignments.

[1] Thomas D. Wu and Serban Nacu
     Fast and SNP-tolerant detection of complex variants and splicing in short reads
     Bioinformatics 2010 26: 873-881