Which Abyss is running? Complete package "Abyss PE"
Memory issues? Shiran confident that RNAseq data would not be an issue.
Can use 256 GB machines for contig
For scaffolding: use BWA or Bowtie to align paired-end reads to primary contigs. More memory efficient than Abyss native k-aligner, which is single threaded.
Need to build modules for BWA and/or Bowtie on Ranger
Wrapper for Abyss shows up as a web-service in the Foundation API in next week (Matt)
FASTQC: Matt has method in place for writing to PDF.
Tallymer--Can use to measure heterozygosity (test using rice, grape, and maize MO17 + B73)