Skip to main content

Table 4 Simulated ReadSet1 analysis where the inputs of EIM pipeline are the read set and either the reference genome (ref) or the genome reconstructed by Bowtie2 (cns-bt)

From: Assessing the impact of exact reads on reducing the error rate of read mapping

c 1 c 2 c 3 c 4 c 5 c 6 c 7
Assembly Exact EIM Exact EIM (v1) EIM (v2) Bowtie2
  /ref /ref /cns-bt /cns-bt /cns-bt / ref
Contigs-500 2817 1 68 9 2 6
N50 (kbp) 1.82 4639.6 156.4 1108.9 3543.3 2385.650
Errors 3 45 0 28 29 38
Genome-Fraction (%) 90.285 100 99.381 99.992 99.999 100
  1. The evaluation metrics has been defined in the text. The columns headed ’Exact/ref’, ’EIM/ref’, ’EIM (v1)/cns-bt’, ’EIM (v2)/cns-bt’ and ’Bowtie2’ represent the contiguity and quality of the respective contigs. Also E. coli K12 genome is denoted by ’ref’ and the consensus sequence constructed by Bowtie2 on E. coli genome is denoted by ’cns-bt’