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
See the Jupyter Notebook for full details of run (see Results section below).
Results:
Output folder: https://owl.fish.washington.edu/Athaliana/20171114_oly_pbjelly/
Output FASTA file: https://owl.fish.washington.edu/Athaliana/20171114_oly_pbjelly/jelly.out.fasta
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