insilicoseq

name	insilicoseq
description	InSilicoSeq — simulate realistic Illumina (meta)genomic reads for benchmarking and experimental design. Use when: (1) Generating Illumina-like test sets from genomes, (2) Simple abundance-controlled mock communities, (3) Complementing CAMISIM for CAMI-style community simulation. Upstream: https://github.com/HadrienG/InSilicoSeq. For full CAMI gold standards prefer cami / CAMISIM.
license	MIT
category	analysis-tools
tags	["simulation","Illumina","benchmark","InSilicoSeq"]
upstream	https://github.com/HadrienG/InSilicoSeq
stage	assessment

InSilicoSeq

Upstream: HadrienG/InSilicoSeq · Docs: https://insilicoseq.readthedocs.io/

Citation

Gourlé, H., Karlsson-Lindsjö, O., Hayer, J. & Bongcam-Rudloff, E. Simulating Illumina metagenomic data with InSilicoSeq. Bioinformatics 35, 521–522 (2019). https://doi.org/10.1093/bioinformatics/bty630

See also docs/references.md.

Analytical thinking

Simulator	Strength
insilicoseq	Fast Illumina metagenome reads; simple CLI
CAMISIM (cami)	Multi-sample designs, strain diversity, CAMI gold standards

Use InSilicoSeq for lightweight tool tests; use CAMISIM/CAMI when you need challenge-grade gold standards for assembly/binning/profiling.

How to run

conda install -c bioconda insilicoseq  # if packaged
iss generate --genomes genome1.fa genome2.fa --model NovaSeq \
  --abundance_file abundances.txt --output temp/iss/mock --n_reads 5M

Related skills

cami · quast · metaphlan · kraken2 · tool-selection