ArticleBioinformatics (Oxford, England)2019
Simulating Illumina metagenomic data with InSilicoSeq.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed.
- Fast and accurate taxonomic domain assignment of short metagenomic reads using BBERT.Nucleic acids research · 2026Article
- Somatic selection shapes mutation accumulation in Citrus sinensis.The Plant cell · 2026Article
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
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- Quantitative comparison of fungal genome assembly strategies using short and long reads from simulated and empirical sequencing data.Microbial genomics · 2026Article
- Benchmarking genomic variant calling tools in inbred mouse strains: recommendations and considerations.Genetics · 2026Article
- Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.mSystems · 2026Article
- Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters inmSystems · 2026Article
- Genestrip: exact and efficient read classification for selected groups of organisms.BMC bioinformatics · 2026Article
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.bioRxiv : the preprint server for biology · 2026Article
- Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.Communications biology · 2026Article
- Sharkmer: repurposing PCR primers for targeted genome assembly using in silico PCR.Bioinformatics (Oxford, England) · 2026Article
- TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.Bioinformatics (Oxford, England) · 2026Article
- ANOMALY: a Snakemake pipeline for identifying NuMTs from long-read sequencing data.NAR genomics and bioinformatics · 2026Article
- A novel simulation tool for low-coverage whole-genome sequencing using multivariate Gaussian mixture models.BMC bioinformatics · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- AmpliFuse: an amplicon simulation tool with enhanced chimera generation for Illumina platforms.Microbiology resource announcements · 2026Article
- A signature-protein-based approach for accurate and efficient profiling of the human gut virome.Cell reports methods · 2026Article
86 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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. Availability and implementation: Source code and documentation are available under the MIT license at https://github.com/HadrienG/InSilicoSeq and https://insilicoseq.readthedocs.io/. Supplementary information: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.