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Table 2 Methylation extraction and calculation of simulated RRBS reads

From: Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data

Tool

Time (hours)

Memory usage (GB)

%Recalla

R2 with Truth from Simulator

BISMARK

1.08

5.78

81.03 %

0.844

BRAT-BW

2.89

2.5

80.46 %

NA

BSMAP

0.4b

3.14b

87.20 %

0.864

BS-SEEKER2

0.54

6.1

73.28 %

0.869

LAST

--

--

78.11 %

0.757

TRACE-RRBS

0.17

7.68

88.59 %

0.988

METHYLCODER

--

--

62.38 %

0.645

NOVOALIGN

1.19

6.2

86.59 %

0.878

  1. aNumber of CpGs with at least 1X coverage divided by total expected CpGs
  2. btime and memory for chromosome 1 as BSMAP script takes a huge amount of memory for whole genome
  3. NA no available script to extract methylation data for the comparison; -- the tools have their methylation extraction script but was not able to be used in this case and an in-house script was used