| 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
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
