Table 2. Program names, versions and options.
| Name | Version | Compression mode | Options |
| SCALCE | 2.3 | fast | -B 1G -T 2 |
| slow | -c bz -T 2 | ||
| dsrc | 1.01 | fast | |
| slow | -l -lm2048 | ||
| SeqSqueeze1 | 1.0(svn) | slow | -h 4 1/5 -hs 5 -b 1∶3 -b 1∶7 -b 1∶11 -b 1∶15 1/20 -bg 0.9 -N -s 1∶1 -s 1∶2 1/5 -s 1∶3 1/10 -s 1∶4 1/20 -ss 10 -sg 0.95 |
| fastqz | 1.5 | fast | e |
| slow | c | ||
| fqzcomp | 4.4 | fast | -n1 -q1 -s1 |
| medium | -n2 -q2 -s6 | ||
| slow | -n2 -q3 -s8+ -b | ||
| quip | 1.1.1 | fast | |
| slow | -a | ||
| sam_comp1 | 0.7 | – | |
| sam_comp2 | 0.3 | – | |
| cramtools | 1.0 | – | –preserve-read-names -L m999 |
| goby | 2.01 | – | -x MessageChunkWriter:codec = hybrid-1–preserve-soft-clips –preserve-read-names –preserve-all-mapped-qualities |
| samtools | 0.1.18 | – | |
| gzip | 1.3.12 | – | |
| bzip2 | 1.05 | – |
Program version names, numbers and common command line options. Additional options were sometimes required to specify the name of the reference used, but this differed per data set.