Next Generation Sequence Analysis Tools

The following packages are installed on Lewis for the analysis of the short sequences generated by next generation sequencing technologies.  For information on how to access these program contact the UMBC.

  1. SOAP, The Short Oligo Analysis Package. SOAP v1 can be used to align short reads to reference sequences, and is also useful for trimming adaptors from the 3' end prior to alignment and counting the numbers of hits.
  2. ABySS, Assembly By Short Sequences A de novo sequence assembler.
  3. Maq: Mapping and Assembly with Qualities Maq vs 0.7.1 is installed.It builds assembly by mapping short reads to reference sequences.
  4. MOSAIK is a reference-guided assembler.