Genome Annotation - Olympia oyster genome annotation results #01

Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.

See that link for run setup and configuration.


Before proceeding further, it should be noted that I neglected to provide Maker with a transposable elements FastA file for RepeatMasker to use.

The following line in the maker_opts.ctl file was originally populated with an absolute path to data I didn’t recognize, so I removed it:

<code>repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner</code>

I’m not entirely sure what the impacts will be on annotation, so I’ve re-run Maker with that line restored (using a relative path). You can find the results of that run here:

Output folder:

Annotated genome file (GFF):

  • [20180807_wqmaker_run_oly_01/Olurida_v081.all.gff (1GB)(

I’d like to post a snippet of the GFF file here, but the line lengths are WAY too long and will be virtually impossible to read in this notebook. The GFF consists of listing a “parent” contig and its corresponding info (start/stop/length). Then, there are “children” of this contig that show various regions that are matched within the various databases that were queried, i.e. repeatmasker annotations for identifying repeat regions, protein2genome for full/partial protein matches, etc. Thus, a single scaffold (contig) can have dozens or hundreds of corresponding annotations!

Probably the easiest and most logical approach from here is to start working with scaffolds that are annotated with a “protein_match”, as these have a corresponding GenBank ID. Parsing these out and then doing a join with a database of NCBI protein IDs will give us a basic annotation of “functional” portions of the genome.

Additionally, we should probably do some sort of comparison of this run with the follow up run where I provided the transposable elements FastA file to see what impacts the exclusion/inclusion of that info had on annotation.