Table 4.
Used Software. Each tool, if applicable, was compiled with optimizations enabled (-O3 -march=native)
| Software | Source | Link | Version |
|---|---|---|---|
| Chopper | This paper | https://github.com/seqan/chopper | 7837f1f |
| Raptor | [12] | https://github.com/seqan/raptor | 560a45f |
| COBS | [10] | https://github.com/bingmann/cobs | 1cd6df2 |
| KMC | [38] | https://github.com/refresh-bio/KMC | v3.2.1 |
| Metagraph | [13] | https://github.com/ratschlab/metagraph | v0.3.6 |
| SeqOthello | [9] | https://github.com/LiuBioinfo/SeqOthello | 68d47e0 |
| HowDeSBT | [18] | https://github.com/medvedevgroup/HowDeSBT | 379f4c8 |
| Jellyfish | [39] | https://github.com/gmarcais/Jellyfish | v2.3.0 |
| Squeakr | [40] | https://github.com/splatlab/squeakr | 0d58134 |
| Mantis | [5] | https://github.com/splatlab/mantis | b6979a2 |
| Bifrost | [7] | https://github.com/pmelsted/bifrost | v1.2.0 |
| Mason | [19] | https://seqan.de/apps/mason | b00001d |
| genome_updater | Vitor Piro | https://github.com/pirovc/genome_updater | v0.3.0 |