SafFire is an interactive tool for visualizing Miropeats genome wise.
Please visit the website to use: https://mrvollger.github.io/SafFire/
To prepare PAF alignments for SafFire, you will need to install rustybam. Once installed you can use the following command to convert your PAF file into a format that SafFire can read:
rb trim-paf {input.paf} `#trims back alignments that align the same query sequence more than once` \
| rb break-paf --max-size 5000 `#breaks the alignment into smaller pieces on indels of 5000 bases or more` \
| rb orient `#orients each contig so that the majority of bases are forward aligned` \
| rb filter --paired-len 100000 `#filters for query sequences that have at least 100,000 bases aligned to a target across all alignments.` \
| rb stats --paf `#calculates statistics from the trimmed paf file` \
> {input.for.saffire}