ReSeq

ReSeq simulates realistic Illumina high-throughput sequencing data. More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original sequences. Snakemake file to reproduce figures and tables in the ReSeq paper. This included the pipeline used to compare ReSeq, pIRS, NEAT and ART on 8 datasets, a bwa bowtie2 comparison with simulated data using ReSeq and various small things. Apply errors and qualities directly to sequences. Even though sequencing biases and errors have been deeply researched to adequately account for them, comparison studies, e.g. for error correction, assembly or variant calling, face the problem that synthetic datasets resemble the real output of high-throughput sequencers only in very limited ways, resulting in optimistic estimated performance of programs run on simulated data compared to real data.