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Meeting notes

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)

Abyss Explorer