Reads Simulation and Read Simulator
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6.1 years ago
midox ▴ 290

hello,

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

reads simulation simulator NGS • 4.0k views
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6.1 years ago
GenoMax 115k

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/

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6.1 years ago

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.

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how introduce errors in the simulator?

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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).

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6.1 years ago
chen ★ 2.4k

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

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

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2.2 years ago
onestop_data ▴ 300

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/

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