Question: Reads Simulation and Read Simulator
0
gravatar for midox
4.9 years ago by
midox260
Tunisia
midox260 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
ADD COMMENTlink modified 12 months ago by onestop_data270 • written 4.9 years ago by midox260
2
gravatar for GenoMax
4.9 years ago by
GenoMax96k
United States
GenoMax96k 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 COMMENTlink written 4.9 years ago by GenoMax96k
1
gravatar for Devon Ryan
4.9 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k 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 COMMENTlink written 4.9 years ago by Devon Ryan98k

how introduce errors in the simulator?

ADD REPLYlink written 4.9 years ago by midox260

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 REPLYlink modified 4.9 years ago • written 4.9 years ago by GenoMax96k
1
gravatar for chen
4.9 years ago by
chen2.1k
OpenGene
chen2.1k wrote:

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

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

ADD COMMENTlink written 4.9 years ago by chen2.1k
0
gravatar for onestop_data
12 months ago by
onestop_data270
onestop_data270 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 COMMENTlink written 12 months ago by onestop_data270
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