<![CDATA[BOL: Minipolish: A tool for Racon polishing of miniasm assemblies]]> https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies? https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies Tue, 03 Dec 2019 02:40:54 -0600 https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies <![CDATA[Minipolish: A tool for Racon polishing of miniasm assemblies]]> Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.

Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.

That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.

It also takes care of some of the other nuances of polishing a miniasm assembly:

  • Adding read depth information to contigs
  • Fixing sequence truncation that can occur in Racon
  • Adding circularising links to circular contigs if not already present (so they display better in Bandage)
  • 'Rotating' circular contigs between polishing rounds to ensure clean circularisation

Address of the bookmark: https://github.com/rrwick/Minipolish

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