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Table 2 The compression ratios of the compared methods on ten test data sets

From: LW-FQZip 2: a parallelized reference-based compression of FASTQ files

  

LW-FQZip 2

LW-FQZip 2 (−g)

LW-FQZip 1

Quip (−a)

Quip (−r)

DSRC 2

CRAM

FQZcomp

LFQC

LEON

SCALCE

bzip 2

gzip

Long-read

SRR2916693

16.7%

15.3%

18.1%

20.9%

20.5%

20.2%

21.9%

21.6%

12.7%

19.5%

17.2%a

24.2%

29.6%

SRR2994368

17.3%

16.0%

17.9%

20.1%

N/A

23.2%

26.4%

N/A

N/A

23.1%

17.3%a

28.5%

34.2%

SRR3211986

33.3%

32.3%

N/A

33.3%

N/A

N/A

33.9%

N/A

32.3%

N/A

33.4%a

36.4%

42.6%

ERR739513

35.2%

34.8%

N/A

N/A

N/A

N/A

35.6%

N/A

34.9%

N/A

N/A

39.7%

45.4%

SRR3190692

12.7%

11.7%

13.2%

16.5%

N/A

20.3%

22.3%

N/A

N/A

18.1%

12.7%a

24.4%

29.5%

Short-read

ERR385912

6.4%

5.0%

6.6%

7.2%

N/A

7.8%

N/A

N/A

5.8%

7.0%

6.6%a

13.9%

17.9%

ERR386131

16.5%

16.0%

18.7%

17.7%

16.6%

16.8%

25.5%

24.6%

15.5%

N/A

16.6%a

21.5%

26.0%

SRR034509

23.7%

22.7%

25.0%

25.1%

24.9%

26.1%

27.4%

26.1%

23.7%

27.9%

24.5%a

31.5%

36.9%

ERR174310

21.0%

20.1%

N/A

20.0%

N/A

20.2%

N/A

N/A

N/A

25.3%

19.6%a

26.2%

31.7%

ERR194147

20.1%

14.3%

N/A

20.0%

N/A

20.3%

N/A

N/A

N/A

20.3%

15.4%a

19.7%

23.6%

  1. Compressed Ratio: the compressed file size divided by the original file size; ‘N/A’: the program cannot work on the data, some error occur in program, such as loses fidelity after decompression or decompression failed; ‘a’: the read order is changed after decompression; The best results are highlighted in bold