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Table 1 Overview of modelled features for the compared simulators

From: ReSeq simulates realistic Illumina high-throughput sequencing data

Coverage Parameters Parameters Parameters Parameters Mapped reads/ Parameters
GC bias Mapped reads Mapped reads Mapped reads
Flanking bias Mapped reads
Fragment length Parameters Parameters Mapped reads Parameters Mapped reads
Reference-sequence bias Hard-coded/(Reads) Mapped reads
Base qualities Reads Mapped reads Reads Reads Mapped reads
Sequence qualities - Mapped reads
Substitution errors Hard-coded Mapped reads Hard-coded Reads Mapped reads
Systematic errors Mapped reads
InDel errors Parameters Mapped reads Hard-coded Reads Mapped reads
Variants Two genomes Vcf Vcf
  1. Parameters: Manually selected parameters. Reads: Learned from raw reads. Mapped reads: Learned from mapped reads. Hard-coded: Cannot be changed. BEAR’s reference-sequence bias estimation from reads is design for metagenomics