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7 votes

How to simulate NGS reads, controlling sequence coverage?

I am working on a Illumina sequencing simulator for metagenomics: InSilicoSeq It is still in alpha release and very experimental, but given a multi-fasta and an abundance file, it will generate reads ...
H. Gourlé's user avatar
5 votes
Accepted

How to simulate nanopore reads?

It is important to train an error model as NanoSim does, as we do not fully understand the error processes involved in both the nanopore sequencing process and the basecalling process. Any sort of ...
conchoecia's user avatar
  • 3,181
5 votes
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After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

I've written a handful of programs from scratch to simulate mutations and variations in real or simulated sequences. The trick has always been to sort the variants by genomic coordinate, apply the ...
Daniel Standage's user avatar
4 votes

How to simulate NGS reads, controlling sequence coverage?

The wgsim package by Heng Li (of BWA and samtools fame) is my go-to tool for simulating Illumina reads. It doesn't provide any convenient way to simulate differential coverage across different ...
Daniel Standage's user avatar
4 votes

How to simulate NGS reads, controlling sequence coverage?

This python script takes a fasta file and tsv file with counts and prints the sequences in the fasta files that many times as it is specified in the tsv file (assuming the format in the question). So ...
Kamil S Jaron's user avatar
4 votes

How to simulate NGS reads, controlling sequence coverage?

The polyester bioconductor package can do this. It says it simulates RNA-seq reads, but I don't know if that's really any different from other NGS reads. It can use a range of error and bias models, ...
Ian Sudbery's user avatar
  • 3,321
4 votes

After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

If you look for a program which would randomly introduce SNPs + short indels and then would save everything into a VCF file, DWGsim or Mason Variator could be a good choice. Then you can create a ...
Karel Břinda's user avatar
4 votes
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GROMACS Coordinates and velocity and force trajectories do not match accuracy

From GROMACS documentation about reproducibility: The following factors affect the reproducibility of a simulation, and thus its output: Precision (mixed / double) with double giving “better” ...
O.Laprevote's user avatar
4 votes
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How to simulate "base error rate" in art_illumina?

You need to specify an error profile to do this. However, you can shift quality scores of an existing profiles to get 10% error, which is easier than defining a complete profile. For example, ...
Mehrdad Bakhtiari's user avatar
3 votes

How to simulate nanopore reads?

I could use NanoSim, but that tool seems to be very difficult to use. I only have a reference genome, but you need training data as well? Karel Břinda's fork, NanoSim-H, ships with pretrained models (...
Mark Amery's user avatar
3 votes
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What are the units for the force output by nstfout, the velocity output by nstvout, and the coordinates output by nstxout in gromacs?

nstxout, nstvout and nstfout are the number of steps between coordinates, speed and forces ...
O.Laprevote's user avatar
3 votes

Introduce errors in reference transcripts according to external dataset error model

This preprint uses pbsim to simulate ONT RNA-seq reads for fruit fly. It is probably worth reading if you want to do the same thing. You should include INDEL errors. Those are what make RNA-seq ...
user172818's user avatar
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3 votes
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Introduce errors in reference transcripts according to external dataset error model

Do any of the answers for this question help? Karel Brinda has mentioned a few read simulators in the answer to that question, and has a thesis with more information. Excluding INDEL errors doesn't ...
gringer's user avatar
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2 votes

How to simulate NGS reads, controlling sequence coverage?

If you're ok with some randomness you can generate reads from your sequence file using a Poisson random variable. You'll need to do some math to figure out what value of lambda to use in order for ...
Greg's user avatar
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2 votes
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How to simulate NGS reads, controlling sequence coverage?

I am not aware of any software that can do this directly, but I would split the fasta file into one sequence per file, loop over them in BASH and invoke ART the sequence simulator (or another) on each ...
Gabriel Renaud's user avatar
2 votes

How to simulate NGS reads, controlling sequence coverage?

Simulating NGS reads while controlling sequence coverage is now easy with RNFtools (from version 0.3.1). See the tutorial, especially section Sequence extraction. Environment preparation First, ...
Karel Břinda's user avatar
2 votes
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Sampling haplotypes

For simple haplotype simulation of unrelated individuals, there is Montana's venerable HapSim. The model used in that tool is simple and may be good enough for your purposes. You will need to acquire ...
winni2k's user avatar
  • 2,286
2 votes

Sampling haplotypes

The data in your matrix appears to be from a VCF file (For reference, see https://github.com/samtools/hts-specs/blob/master/VCFv4.3.pdf). In the VCF specification, a heterozygous genotype can be ...
winni2k's user avatar
  • 2,286
2 votes
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RSVSim insertions from chr1 to chr2

Answer eventually found on the BioConductor post: https://support.bioconductor.org/p/114354/#114585 It basically comes down to not using RSVSim, but other R packages. Final code snippit: ...
Fini's user avatar
  • 153
2 votes

Generating simulated gold standard NGS dataset/ Any publicly available smal gold standard NGS dataset

I would suggest subsampling an existing dataset such as the GIAB resource that you've already indicated. Use a utility such as seqtk to subsample the appropriate number of reads from the dataset, and ...
Maximilian Press's user avatar
1 vote
Accepted

building complex drug-dna for AMBER software

the tutorials video on youtube Gromacs has great written documentation, so I'd suggest referring to that directly. I can also use GROMACS if that gives me the results. Gromacs works fine with a DNA-...
Matteo Ferla's user avatar
  • 4,244
1 vote

How to modify DNA evolution model to fit actual data?

I decided that this was too involved for a comment, so I'm making it an answer. It is still quite difficult to answer the question given the absence of methods explanation; but I think that there's ...
Maximilian Press's user avatar
1 vote

How to modify DNA evolution model to fit actual data?

Mutation is not a random process because there are many mutational biases, e.g. the transition vs. transversion ratio. Ideally use a proper evolutionary model. Maybe try a tool that incorporates ...
Chris_Rands's user avatar
  • 3,948
1 vote
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How to simulate phenotype from real genetic data for GWAS purpose?

The question has been answered in the bioStars forum: https://www.biostars.org/p/428314/ It was missing the param --simu-causal-loci. I created the ...
Bruno Ambrozio's user avatar
1 vote

Simulating 3' end tag-based scRNA-seq reads

Looks like a couple options have become available: Minnow: article code scReadSim: preprint code
merv's user avatar
  • 651
1 vote

Introduce errors in reference transcripts according to external dataset error model

The executable fastq-sim in DNemulator package is able to modify a set of input sequences in fasta format according to an ...
aechchiki's user avatar
  • 2,676
1 vote

Introduce errors in reference transcripts according to external dataset error model

It sounds like what you're really looking for is a read simulator. A cursory search turns up NanoSim, which is designed to simulate reads from a MinION. This has the benefit of at least having been ...
Devon Ryan's user avatar
  • 19.7k

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