kdm9 / miniprothint

Miniprothint selects a set of reliable gene prediction hints from miniprot alignments scored by miniprot boundary scorer.

Miniprothint

Miniprothint selects a set of reliable gene prediction hints from miniprot alignments scored by miniprot boundary scorer.

Usage

We recommend running miniprot and miniprot boundary scorer separately for easier debugging:

miniprot genome.fasta proteins.fasta --aln > miniprot.aln
miniprot_boundary_scorer -o miniprot_parsed.gff -s blosum62.csv < miniprot.aln
miniprothint.py miniprot_parsed.gff --workdir miniprothint

Coming soon

However with a protein fasta file on input, miniprothint can take care of running miniprot and miniprot boundary scorer:

miniprothint.py --genome genome.fasta --proteins proteins.fasta --workdir miniprothint

or just miniprot boundary scorer:

miniprot genome.fasta proteins.fasta --aln > miniprot.aln
miniprothint.py --alignment miniprot.aln --workdir miniprothint

If the latter two ways of running miniprothint are used, miniprot and miniprot boundary scorer must be in the $PATH.

Outputs

• miniprothint.gff A set of hints passing a relaxed set of thresholds.
• hc.gff A set of hints passing stringent thresholds.

If miniprot and/or miniprot boundary scorer are run by miniprothint, their outputs are saved to:

• miniprot.aln
• miniprot_parsed.gff