Reads Simulation and Read Simulator

Question: Reads Simulation and Read Simulator

4.9 years ago by

midox • 260

Tunisia

midox • 260 wrote:

hello,

Can you explain me what's a reads Simulation or Read Silulator? and what's the simulation data or Reads? Thanks

ngs simulation simulator reads • 3.2k views

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modified 12 months ago by onestop_data • 270 • written 4.9 years ago by midox • 260

4.9 years ago by

GenoMax ♦ 96k

United States

GenoMax ♦ 96k wrote:

Following description is from ART website but you can replace word ART with any other simulation program

ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery.

http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

ADD COMMENT • link written 4.9 years ago by GenoMax ♦ 96k

4.9 years ago by

Devon Ryan ♦ 98k

Freiburg, Germany

Devon Ryan ♦ 98k wrote:

A read simulator takes a sequence and generates fake fastq files from it. These generally will have an error profile vaguely similar to that actually seen on a (typically Illumina) sequencer.

ADD COMMENT • link written 4.9 years ago by Devon Ryan ♦ 98k

how introduce errors in the simulator?

ADD REPLY • link written 4.9 years ago by midox • 260

If you are using one of the available simulation programs then it should have options to introduce errors. If this question is about simulating MinIon (which is what you seems to work with) reads then I have not seen a program for that (which does not mean one does not exist).

ADD REPLY • link modified 4.9 years ago • written 4.9 years ago by GenoMax ♦ 96k

4.9 years ago by

chen • 2.1k

OpenGene

chen • 2.1k wrote:

https://github.com/OpenGene/SeqMaker.jl

Next Generation Sequencing simulation with SNP, Variation and Sequencing Error Integrated

ADD COMMENT • link written 4.9 years ago by chen • 2.1k

12 months ago by

onestop_data • 270

onestop_data • 270 wrote:

I have written this tutorial on how to simulate reads for single-cell genomes and metagenomics. It covers how to simulate Illumina (NovaSeq, HiSeq or MiSeq), Pacific Biosciences (PacBio) SMRT, and Oxford Nanopore reads.

https://onestopdataanalysis.com/read-simulator/

ADD COMMENT • link written 12 months ago by onestop_data • 270

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