More Jellyfish

This class we discussed the results from the Jellyfish run on Pyrobaculum oguniense. John St. John joined us and suggested some other tools to consider.

• ABySS [1]
  • An assembler with modest memory requires. May be runnable on campusrocks.
  • Good support through active user group.
• SGE
• SeqPrep
  • A tool for read clean up that scans paired end reads for adapter sequences.

We set the goal of running Jellyfish on the Illumina slug data to estimate the genome size and error rates from the coverage. We will use a beta version of Jellyfish with support for FASTQ formatted input and write a simple script to translate QSeq formatted sequences to FASTQ format.