MetaSim protocols

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MetaSim specifications

Information


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

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Publication for MetaSim

MetaSim in pipelines

 (3)
2015
PMCID: 4309676
PMID: 25673967
DOI: 10.4137/EBO.S20523

[…] lastly, we evaluated the effectiveness of outliers on wsvdd and other classifiers. in all experiments, the testing sequences and training sequences were generated by read simulation software metasim.27, the training genomes and test genomes were downloaded from the us national center for biotechnology information (ncbi) in september 2011. taxonomic information for each genome […]

2013
PMCID: 3597637
PMID: 23516532
DOI: 10.1371/journal.pone.0058669

[…] genomes. the reference genome sequences were downloaded from the ncbi ftp site. the site also contains the annotation files of cog-cds locations on the genomes., we used a sequencing simulator, metasim (version 0.9.5) , to generate the sequencing reads. this simulator takes into account the sequencing error and has options of different technology platforms (we chose 454 sequencing reads […]

2012
PMCID: 3510651
PMID: 23192148
DOI: 10.1038/nature11650

[…] matched 92% of publicly available wheat full-length cdnas and 78.7% of harvests (), indicating they represent nearly all wheat genes., we optimized parameters for wheat gene assembly using metasim to generate simulated 5× 454 reads from the allotetraploid maize genome and from a triplicated rice gene set, with the introduction of sequence variation (). similar degrees of coverage […]


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MetaSim in publications

 (54)
PMCID: 5943621
PMID: 29774017
DOI: 10.3389/fmicb.2018.00872

[…] 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 […]

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

[…] real datasets used come from other papers ([, , ]) and we summarize them in the next section., 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 […]

PMCID: 5698827
PMID: 29250541
DOI: 10.1155/2017/4740354

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]


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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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