Tools to simulate Illumina short read sequences and ONT long reads with a reference genome

Question

[PolenP]

Hi, I would like to ask if you can recommend me tools that I can use to simulate whole genome sequences using a reference genome which will also give me list of the variants just like wgsim?

I was able to use wgsim, but when I tried aligning the paired-reads, it's not aligning together.

reads=100000000

for i in $(seq 1 10); do
  base="sim_${i}"
  seed=$((100 + i))   # different seed for each run (arbitrary choice)
  echo "Running $base  (seed=$seed)..."
  "$wgsim" "$ref" "${base}.R1.fq" "${base}.R2.fq" -1 70 -2 70 -N $reads -S $seed -e 0.0001 > "${base}.out.log" 2>&1
  echo "$base finished (log: ${base}.out.log)"
done

of maybe I am using wgsim wrong? I hope you can help me. Thank you!

[cmdcolin]

It's a little unclear what you mean by "I was able to use wgsim, but when I tried aligning the paired-reads, it's not aligning together."

[PolenP]

Sorry about that. It's when I align the paired reads together like the left and righ, they should align with common sequence at some ends, making one longer consensus sequence. I was able to align the pairs with an actual short read pairs.

Answer 1

[colindaven]

The best one I've used for ONT reads so far is badread - https://github.com/rrwick/Badread

For illumina I've used and like insilicoseq - https://insilicoseq.readthedocs.io/en/latest/

[GenoMax]

which will also give me list of the variants

Do either of these packages satisfy the requirement of generating known mutations?

Answer 2

[Mensur Dlakic]

You may want to consider one of these packages:

• https://www.niehs.nih.gov/research/resources/software/biostatistics/art
• https://github.com/YU-Zhejian/art_modern

[GenoMax]

Do you know if ART is able to generate known mutations.

[Mensur Dlakic]

I think only a fraction of sequencing errors can be specified. If a mix of a reference and a mutated genome is included, setting sequencing errors to 0 might give reads with fixed mutations.

Answer 3

[GenoMax]

if you can recommend me tools

You can use randomreads from BBMap suite to generate short illumina reads with known mutations. A guide is available here: https://bbmap.org/tools/randomreads