Comments (1)
This may not require fixing in this pipeline. A typical fasta header from a dragonflye assembly looks like this:
>SAMPLE_contig00001 len=5468462 cov=46.0 origname=contig_1_polypolish polish=racon:1 round(s);polypolish:short_reads,1 round(s); sw=dragonflye-flye/1.1.0 date=20230621 circular=Y
A typical fasta header from a unicycler assembly looks like this:
>SAMPLE_1 length=728413 depth=1.00x
This issue was prompted by the fact that the full dragonflye header appears in the resistance_gene_contig_id
in the output of our BCCDC-PHL/plasmid-screen pipeline. But it appears that may be caused by some downstream parsing logic in that pipeline or maybe in mob-suite.
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Related Issues (6)
- Quast output includes N90 / L90 metrics but parse_quast_report.py expects N75 / L75 metrics HOT 2
- Add plasmid rotation, similar to Unicycler
- Optionally convert `circular=Y` to `circular=true` in fasta headers
- Add support for 'collecting' csv/tsv outputs
- Add support for `--plasmids` and `--meta` flye flags HOT 2
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