How to find sequence variations from contigs

• RagTag

  5 430 0.0 Python

  Tools for fast and flexible genome assembly scaffolding and improvement

My first idea was to assemble the contigs into scaffolds (e. g. using RagTag) and then look for a tool that can identify these mutations. However, I've also come across snippy, which is a tool that can identify mutations from reads. I don't know if I can just apply it to contigs though (probably not).

• snippy

  6 436 3.9 Perl

  :scissors: :zap: Rapid haploid variant calling and core genome alignment

My first idea was to assemble the contigs into scaffolds (e. g. using RagTag) and then look for a tool that can identify these mutations. However, I've also come across snippy, which is a tool that can identify mutations from reads. I don't know if I can just apply it to contigs though (probably not).

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• dipcall

  1 86 0.0 JavaScript

  Reference-based variant calling pipeline for a pair of phased haplotype assemblies

dipcall. Use the same contig file as both parents.

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