Skip to main content

Table 1 Summary of characteristics of read-length distributions and quality profiles for BEAR and popular sequencing simulator programs

From: A better sequence-read simulator program for metagenomics

Program Read length distribution Quality profiles Errors
MetaSim Uniform and Normal Not generated User-defined, parametric
SimSeq Uniform High quality for first 80bp, low quality after User-defined, parametric
Grinder Uniform and Normal Binary; either "good" or "bad" User-defined, parametric
454sim Uniform Highly sensitive to parameter settings User-defined, parametric
GemSIM Non-parametric Non-parametric Inferred from alignment to reference genome
BEAR Non-parametric Non-parametric for correct base calls, second-degree polynomial for errors Inferred from log regression analysis of clustering artifactual duplicate reads within data