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Citations per year

Number of citations per year for the bioinformatics software tool MetaSim

Tool usage distribution map

This map represents all the scientific publications referring to MetaSim per scientific context
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MetaSim specifications


Unique identifier OMICS_01509
Name MetaSim
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Known genome sequences
Input format FASTA
Output data A collection of reads sequences.
Output format MULTIFASTA (optionally compressed)
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 0.9.5
Stability Stable
Maintained Yes




No version available


Publication for MetaSim

MetaSim citations


Identifying Group Specific Sequences for Microbial Communities Using Long k mer Sequence Signatures

Front Microbiol
PMCID: 5943621
PMID: 29774017
DOI: 10.3389/fmicb.2018.00872

[…] roup than in the patient group. The remaining nine genomes have identical abundance distributions between the healthy individual and the patient groups. The detail setting is shown in Table . We used MetaSim () to generate 15 metagenomic samples for case and control groups, respectively. For each group, the absolute values of Gaussian noises of mean zero and standard derivation equal to each centr […]


CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision

BMC Bioinformatics
PMCID: 5751405
PMID: 29297295
DOI: 10.1186/s12859-017-1967-3

[…] mic datasets of 10 genomes with different relative abundances have been used in evaluation of MaxBin []. Generation of 5 million and 20 million Illumina reads from the sample has been simulated using Metasim reads simulator and assemblies have been generated using Velvet assembler []. The two sets of assemblies of different overall coverages, 20x and 80x and their coverage profiles were downloaded […]


Higher recall in metagenomic sequence classification exploiting overlapping reads

BMC Genomics
PMCID: 5731601
PMID: 29244002
DOI: 10.1186/s12864-017-4273-6

[…] For our test we used 16 sets of simulated short read datasets used also in []. These are generated with MetaSim software and they can be partitioned in two groups: S and L. Each dataset comprises paired-end short reads (length of approximately 80 bp) generated according to the Illumina error profile wit […]


Gene Prediction in Metagenomic Fragments with Deep Learning

Biomed Res Int
PMCID: 5698827
PMID: 29250541
DOI: 10.1155/2017/4740354

[…] DNA sequences from different sequencing technologies, the genome sequences in training dataset are randomly split into 700 bp and 120 bp fragments with 1-fold genome coverage for each genome, and the Metasim [] is used to generate 700 bp and 120 bp fragments with the 3-fold genome coverage for each genome in the testing dataset. Now that the purpose of metagenomics gene prediction is to discrimina […]


Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses

PLoS One
PMCID: 5407692
PMID: 28448616
DOI: 10.1371/journal.pone.0176154

[…] published dataset of real gut metagenomes from the Chinese population []. The R package HMP [] was used to generate random read counts from these distributions; then, the read counts were inputted to MetaSim [] to produce 20 metagenomic readsets.During the comparison, the relative abundance levels in the simulated metagenomes were calculated for a gene group of ribosomally synthesized and post-tra […]


A framework for space efficient read clustering in metagenomic samples

BMC Bioinformatics
PMCID: 5374685
PMID: 28361710
DOI: 10.1186/s12859-017-1466-6

[…] datasets have realistic error rates, contain up to a hundred species, and have different fractions of low-abundance species. The datasets are created by feeding the reference genomes from NCBI to the Metasim software by []. Third, we pick two real samples: a sample from the human gut catalogue described in [] containing 1.4 billion base pairs, and a sample from a study on the mouse gut described i […]

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MetaSim institution(s)
ZBIT- Center for Bioinformatics Tübingen, University of Tübingen, Tubingen, Germany; Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany

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