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 Unfortunately, most current read simulators are either not suited for metagenomics, out of date or relatively poorly documented.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

SLU Authors

• Gourlé, Hadrien

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

• Karlsson Lindsjö, Oskar

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Hayer, Juliette

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

• Bongcam Rudloff, Erik

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Bioinformatics (Computational Biology)


Publication identifier

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

Permanent link to this page (URI)

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