Yesterday, I ran PB Jelly using Sean’s Platanus assembly, but that didn’t produce an assembly because PB Jelly was expecting gaps in the Illumina reference assembly (i.e. scaffolds, not contigs).
Re-ran this using the BGI Illumina scaffolds FASTA.
Here’s a brief rundown of how this was run:
- Default PB Jelly settings (including default settings for blasr).
- Illumina reference FASTA: BGI Illumina scaffolds FASTA
- PacBio reads for mapping
- Protocol.xml file needed for PB Jelly to run
See the Jupyter Notebook for full details of run (see Results section below).
OK! This seems to have worked (and it was quick, like less than an hour!), as it actually produced a FASTA file! Will run QUAST with this and some assemblies to compare assembly stats. Have added this assembly to our Olympia oyster genome assemblies table.
Jupyter Notebook (GitHub): 20171114_emu_pbjelly_BGI_scaffold.ipynb