Genome Assembly - Olympia Oyster Illumina & PacBio Using PB Jelly w/BGI Scaffold Assembly

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.

• PB Jelly Documentation

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).

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