Table 2.
FASTQ processing tools overview
| Valid | Invalid | Process .gz | Plain (reads/s) | Compressed (reads/) | |
|---|---|---|---|---|---|
| fqtools | Y | Y | R+W | 701 375 | 444 648 |
| bash | — | — | R+W | 2 605 421 | 934 331 |
| bioawk | Y | N | R | 434 632 | 312 708 |
| seqtk | Y | N | R | 1 122 355 | 545 865 |
| fast | Y | Y | — | 2984 | — |
| fastx-toolkit | N | N | — | 69 762 | — |
| seqmagick | Y | Y | R+W | 25 325 | 4000 |
Benchmark data for various FASTQ processing tools. All tools were installed locally, and run against the complete test set (Cock et al., 2010). Valid shows if all the valid test set were processed correctly. Invalid shows if the tool identified all the invalid files. Process .gz shows if the tool can natively read (R) and write (W) gzip-compressed files. The speed columns show the speed in reads per second.