HTS Compression Benchmark Suite
Compression Tools
This repository contains the binaries of compression tools used for HTS Compression Benchmark.
Unless otherwise specified, all executables are exactly those ones we used in the paper. Because of library dependencies, some tools had to be re-compiled for AWS. All manually compiled tools were compiled with gcc 4.8 or 5.2.
Please refer to Benchmarking Quickstart for more information how to set up benchmarking environment.
| Name | Release | Note |
|---|---|---|
| pigz | 2.3.3 | |
| pbzip2 | 1.1.12 | Uses bzip2 1.0.6 Recompiled for Ubuntu |
| Cramtools | 0c89dd8 | Needs Java |
| Scramble | 1.14.6 | Uses bzip2 1.0.6 Recompiled for Ubuntu |
| Sambamba | 0.6.0 | |
| Samtools | e2bb18f | Uses htslib 897a34f |
| sam_comp | 0.10 | |
| CBC | d18afbb | |
| Picard | 1.138 | Needs Java |
| Quip | 629f6fc | |
| DeeZ | abc6dc8 (v1.9 beta 1) | Recompiled for Ubuntu |
| Fqzcomp | 4.6 | |
| DSRC2 | 5eda82c | Recompiled for Ubuntu |
| Fastqz | 15 (39b2bbc) | Recompiled for Ubuntu |
| Slimfastq | f55ae88 | Recompiled for Ubuntu |
| BEETL | 6c240ea | |
| ORCOM | 6280813 | Recompiled for Ubuntu |
| LFQC | ? 1.1 (b6bc1b8) | |
| kPath | 0.6.3 | |
| Mince | 3ddc3a1 | Compiled from scratch |
| LW-FQZip | 1.02 | Source edited to use system tar |
| FQC | 3.0c | |
| Leon | 1.0.0 | |
| SCALCE | v2.8 (ef1bc4c) | Uses zlib 1.2.8 and pigz 2.3.3 |