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A package to facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects. MetaSim can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies.

BEAR / Better Emulation for Artificial Reads

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It is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads with read lengths, quality scores, error profiles, and species abundances derived from real user-supplied WGS data. BEAR can emulate reads from various sequencing platforms, including Illumina, 454, and Ion Torrent. BEAR requires minimal user input, as it automatically determines appropriate parameter settings from user-supplied data. BEAR also uses a unique method for deriving run-specific error rates, and extracts useful statistics from the metagenomic data itself, such as quality-error models.