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Research article - Peer-reviewed, 2019

Simulating Illumina metagenomic data with InSilicoSeq

Gourle, Hadrien; Karlsson-Lindsjo, Oskar; Hayer, Juliette; Bongcam-Rudloff, Erik

Abstract

Motivation: The accurate in silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation of computational needs within a project. Unfortunately, most current read simulators are either not suited for metagenomics, out of date or relatively poorly documented. In this article, we describe InSilicoSeq, a software package to simulate metagenomic Illumina sequencing data. InsilicoSeq has a simple command-line interface and extensive documentation.Results: InSilicoSeq is implemented in Python and capable of simulating realistic Illumina (meta) genomic data in a parallel fashion with sensible default parameters.

Published in

Bioinformatics
2019, volume: 35, number: 3, pages: 521-522
Publisher: OXFORD UNIV PRESS

Authors' information

Gourlé, Hadrien
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Karlsson Lindsjö, Oskar
Swedish University of Agricultural Sciences, Department of Molecular Sciences
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Bongcam-Rudloff, Erik (Bongcam Rudloff, Erik)
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Bioinformatics (Computational Biology)

Publication Identifiers

DOI: https://doi.org/10.1093/bioinformatics/bty630

URI (permanent link to this page)

https://res.slu.se/id/publ/99031