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Table 1 Performance comparisons for mapping simulated RRBS reads to RR and WG indexes

From: BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

  Error-free Error-containing
To RR   To WG To RR   To WG
Mappability 74.04% 72.52% 74.41% 72.95%
User time 1m23s 4m18s 1m20s 4m37s
Accuracy 100.00%   100.00% 99.33% 97.92%
  1. 100 k reads of length 50 bp are simulated from the RR genome. Mapping is done using BS-Seeker2 (Bowtie). Mapping to the reduced represented (RR) index is much faster than mapping to the whole genome (WG) index. For error-free samples, the mappability to RR is higher than WG by avoiding pseudo-multiple hits. For error-containing samples, mapping to the RR index will result in higher accuracy than mapping to the WG index. Arrows indicate the improvement directions.