Details coming soon
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).
- Dealing with long running times.
- Set the filter level.
- Run terminator on checkpoint files.
- Iterate using short mates before long.