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Table 1 Summary of bamchop test runs

From: Efficient digest of high-throughput sequencing data in a reproducible report

Source

Sequencer

Aligner

Paired-end

Avg. length (bp)

Total bases (million)

Total bases (billion)

BAM size (gb)

Runtime (minute)

1000 Genomes

454

MOSAIK

No

332.10

1.24

0.41

0.15

8.33

1000 Genomes

454

ssaha

No

390.00

9.81

3.83

3.31

11.66

CHOP project

SOLiD

Tophat

No

50.00

35.93

1.80

1.77

13.62

1000 Genomes

Illumina

maq

Yes

76.00

14.60

1.11

2.00

13.99

CHOP project

SOLiD

LifeScope

No

47.71

52.26

2.49

4.09

18.76

1000 Genomes

Illumina

maq

Yes

51.00

106.70

5.44

8.25

23.91

CHOP project

Illumina

Novoalign

Yes

92.92

226.50

21.05

28.89

33.13

1000 Genomes

Illumina

maq

Yes

37.00

192.02

7.10

11.10

34.25

CHOP project

Illumina

Novoalign

Yes

93.34

239.21

22.33

30.73

34.29

  1. BAM files generated by local projects or 1000 Genome project using different sequencing instruments and alignment programs were tested with bamchop. The average mapping length, total number of aligned reads and bases, BAM file size, and time taken to finish each run were summarized in this table, which showed that the number of reads is the primary factor determining runtime.