Best Practices

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Details coming soon

November 2014

Assembling long reads

  • Do not shred the reads.
  • Set the BITS field in the AS_global.h file before compile. It was 11 in CA7 and 15 in CA8.
  • As of CA8, when running fastqToCA, set the PacBio read type.
  • Optionally run pacBioToCA to correct PacBio reads before assembly. Set error thresholds to ~6%.
  • Another option is to assemble PacBio reads without correction. Set error thresholds to ~40%.

Assembling long and short reads

  • In the spec file, list short read files (e.g. Illumina.frg) before long read files (e.g. PacBio.frg).

Trimming

Scaffolder

  • Dealing with long running times.
  • Set the filter level.
  • Run terminator on checkpoint files.
  • Iterate using short mates before long.