Skip to main content

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