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Table 1 Summary of SV detection tools.

From: iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data

Tool

Algorithm

Detectable SV types

Simulation 30× CPU time, max. memory size

NA12878 45× CPU time, max. memory size

BD

RP

DEL, INS, INV, TRA

1.6h, 0.3Gb

2.1h, 0.5Gb

Delly

RP, RD, SR

DEL, INV, DUP, TRA

1.3h, 0.5Gb

24h, 9Gb

Pindel

SR

DEL, INS, INV, DUP, TRA

19h, 3Gb

37h, 3Gb

HC

AS

DEL, INS, other

68h, *9Gb

180h, *9Gb

  1. SV detection tools are summarized according to algorithm types, detectable SV types, and computational resources required in our analyses. For each tool, CPU time and maximum memory size were measured for the 30× simulation data and the 45× whole genome sequence data of NA12878. RP, RD, SR, and RP stand for read pair, read depth, split read, and assembly approaches, respectively. 'BD' is BreakDancer. HC, Haplotype Caller; 'DEL', deletion; 'INS', insertion; 'INV', inversion; 'DUP', duplication; 'TRA', translocation.
  2. * HC was performed with explicitly specified maximum memory size.