Question

Mutate genomes in silico

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2.1 years ago

biobiu ▴ 150

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 • 1.1k views

ADD COMMENT • link 2.1 years ago by biobiu ▴ 150

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

ADD REPLY • link 2.1 years ago by iraun 6.2k

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The genome sequences, Thanks

ADD REPLY • link 2.1 years ago by biobiu ▴ 150

score 3 · Answer 1 · 2022-10-14

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2.1 years ago

iraun 6.2k

BamSurgeon for spiking mutations into the reads.

snp-mutator for fasta files.

ADD COMMENT • link 2.1 years ago by iraun 6.2k

score 2 · Answer 2 · 2022-10-15

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2.1 years ago

shenwei356 8.7k

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.

ADD COMMENT • link 2.1 years ago by shenwei356 8.7k

score 1 · Answer 3 · 2022-10-15

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.