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Mutate genomes in silico

Hello, I'm looking for a tool that might introduce mutations to genomes. The main idea is to test how mutations will affect mapping (both genome to genome, and short reads to genome). Any recommendations please? Have a great weekend!

genome
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written by biobiu biobiu

You mean to mutate a fasta (genome sequence) or a fastq (reads) file?

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written by iraun iraun

The genome sequences, Thanks

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written by biobiu biobiu

3 answers

BamSurgeon for spiking mutations into the reads.

snp-mutator for fasta files.

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written by iraun iraun

Try simutator, e.g., every 2kb where a region of length 1.5kb gets 30 snps, 2 insertion and 4 deletions up to length 10bp.

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written by shenwei356 shenwei356

mutate.sh from BBMap suite. Take a look at in-line help for additional options.

Written by Brian Bushnell
Last modified August 6, 2019

Description:  Creates a mutant version of a genome.

Usage:  mutate.sh in=<input file> out=<output file> id=<identity>

I/O parameters:
in=<file>       Input genome.
out=<file>      Output mutant genome.
vcf=<file>      Output VCF file showing variations added.
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written by GenoMax GenoMax

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