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simulating illumina data with spiked variants

Hi all,

I am looking to simulate some paired illumina data for a test. What I want to do in order of importance (most important at the top)

  1. Create fastq files.
  2. Specify specific SNPs to be in the data
  3. Control the allelic fractions of the spiked in SNPs
  4. Have an appropriate error model of illumina sequencing
  5. Have controllable metrics like duplicate rate, chastity fail rate

There seem to be a number of tools available for simulating illumina - do we know of one that can handle my requirements?

simulated-data illumina
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updated by Ram Ram • written by Richard Richard

2 answers

Aside from #5, any of the common simulators (wgsim, Sherman, etc.) can do that. For the SNPs, just make a second genome containing them, sample from that as well, and then mix the results in the fraction that you'd like.

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written by Devon Ryan Devon Ryan

I checked both wgsim and sherman and I didn't see a way to spike in specific variants (base change and position). Am I missing something?

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written by Richard Richard

Read the entirety of my answer, I mentioned the variants explicitly.

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written by Devon Ryan Devon Ryan

For 1, 2 (maybe 3), 4 we developed a sequencing simulator for ancient DNA: grenaud.github.io/gargammel/ But it can be used to simulate modern DNA. For the PhiX, you can add it as a "microbial contaminant". It automates the process of fragment size distribution, sampling from a diploid genome and generate Illumina-like fastq files. Just give it a "diploid" genome represented by 2 fasta files.

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written by Gabriel R. Gabriel R.

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