Next Generation Sequence Analysis Tools

The following packages are installed on Lewis and/or Clark for the analysis of the short sequences generated by next generation sequencing technologies.  They are accessible from the commmand line.

  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.   For help in submitting a SOAP job on lewis go here.
  2. Maq: Mapping and Assembly with Qualities Maq vs 0.7.1 is installed.It builds assembly by mapping short reads to reference sequences.
  3. MOSAIK is a reference-guided assembler.
  4. The "Tuxedo Suite" of Bowtie, Tophat, and Cufflinks, is available on Lewis for the analysis of differential gene expression, discovery of splice forms, and fast alignment of short reads.  See here for directions.
  5. Velvet is installed on clark.  It is a sequence assembler for short reads but also allows the inclusion of longer length sequences.  For more about running VELVET go here.
  6. ABySS, Assembly By Short Sequences A de novo sequence assembler.
  7. VCAKE "is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data."
  8. SSAKE "The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree.  SSAKE is designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets."
  9. Edena "(Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm."