Hi, I have a simulation in .fasta format, I want to generate simulate read that has 40x coverage, I know the number of read I should generate, but wgsim do not seem to provide such option. Is there any tool I could use to generate such read? Thanks!
The -N parameter let's you set the number of reads. Then, in addition, the -1 and -2 flags allow you to set the read length.
The above parameters together provide you with full control over the average coverage of the simulated reads.
ART can simulate outputs of many different sequencing platforms, and has an option to specify coverage.
randomreads.sh from BBMap suite can do coverage based read generation. You can do many other things like add mutations etc. Run the program by itself to see options.
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