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Table 5 Comparison of computational time on the simulation dataset with 100 individuals, STR mutation rate of 2.73 × 104, and read coverage of 40 × and the real dataset for HapMap JPT individuals

From: Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree

Method

Computational time

Computational time

 

(simulation data)

(real data)

CoalescentSTR (sampling)

13372.96 [s]

846.60 [s]

CoalescentSTR (estimation)

452.59 [s]

66.86 [s]

Basic Model

49.58 [s]

16.18 [s]

lobSTR

2.72 [s]

8.17 [s]

RepeatSeq

10.24 [s]

14.78 [s]

STRViper

407.03 [s]

83.45 [s]

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BMC Genomics

ISSN: 1471-2164

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