Table 1 Time-consuming from five software on human HEK293 samples in silico
From: Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform
Software/version | Character of building index | Indexing strategy | Alignment softwarea | Strategy | Final report? | Sample data (pair-end reads/Mb) | Time of building reference index | Alignment/h | Deduplication | Extraction of paired_read | Extraction of methylation | Total time |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
BSMAP v2.90 | Building reference index in process of alignment | Hash tables | SOAP | Wild-card | No | 105.675 p = 0.0013 | 0 | 10.478 p = 0.0014 | 24.5 (m) p = 0.0007 | 0 | 33 (m) p = 0.0001 | 11h26m |
Bismark v0.22.3 | Building multi-reference index at a time | FM index | bowtie2 | 3-letter | Yes | 1h51m | 7.025 p = 0.0015 | 35 (m) p = 0.0019 | 100 (m) p = 0.0010 | 7.15 (h) p = 0.0008 | 18h26m | |
BatMeth2 | Building one reference index at a time | FM index | BatMeth2 | 3-letter | Yes | 2h42m | 13.07 p = 0.0017 | 113 (m) p = 0.0109 | 17h39m | |||
BS Seeker2 v2.1.0 | Building one reference index at a time | FM index | bowtie2 | 3-letter | No | 3h17m | 111.08 p = 0.0011 | 36 (m) p = 0.0003 | 0 | 30.85 (h) p = 5.236e-05 | 145h44m | |
BSBolt v1.4.8 | Building one reference index at a time | FM index | BWA-MEM | 3-letter with forked version of BWA-MEM and HTSLIB | No | 2h18m | 7.775 p = 0.0059 | 47 (m) p = 0.0025 | 0 | 7 (m) p = 0.0022 | 10h58m | |