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Table 4 Comparison of performance for selecting reads with base at a sequence position (nt)

From: BAMQL: a query language for extracting reads from BAM files

 

System

User

Wall

Code

Tool

time (s)

time (s)

time (s)

(bytes)

BAMQL

3.55

109.16

115.69

54

C

2.89

107.49

114.17

2590

Perl

3.73

264.84

356.29

1667

Python

4.24

137.06

171.77

1225

SAMtools+AWK

41.42

2591.00

2322.19

831

Sambamba+AWK

56.12

3446.93

3100.96

874

  1. Best performer is highlighted in bold