I've got a little new tool to share: Minipolish
github.com/rrwick/Minipol…
It does Racon-polishing on a miniasm long-read assembly. Why not just use Racon directly? For a few reasons...
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1. Minipolish keeps the assembly in graph form (GFA format) whereas Racon produces FASTA sequences.
2. Racon has a nasty habit of sometimes truncating sequences a little bit when it polishes them - Minipolish will repair this.
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3. Minipolish 'rotates' circular contigs (like in bacterial genomes) between polishing rounds. This ensures that final polished contigs circularise cleanly (no missing or overlapping bases).
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4. Minipolish will add read depth information to the contigs. This can help distinguish important high-depth contigs from other low-depth stuff.
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Despite its relative simplicity, I've found miniasm to be a great little assembler that can hold its own against the more robust tools like Flye and Canu. By simplifying the polishing process, I hope Minipolish makes miniasm easier to use!
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As always, thank you to all the other bioinformaticians out there for their work! Especially @lh3lh3 for miniasm and the Racon developers (@IvanSovic, @robertvaser and @msikic).
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