Software used in this pipeline
We gratefully acknowledge the trememdous efforts put in by many developers without whose work GABI would not exist. For a list of packages used in this pipeline, please see the (hopefully comprehensive) list below. For the very latest versions and tools used, please consult the pipeline report.
| Tool | Version | License* | Url | DOI |
|---|---|---|---|---|
| Abricate | 1.0.1 | GPL 2.0 | link | |
| AMRFinder Plus | 3.11.18 | Public Domain | link | link |
| Autocycler | 0.6.2 | GPL 3.0 | link | link |
| Bracken | 2.9 | GPL 3.0 | link | |
| BTyper3 | 3.4.0 | GPL 3.0 | link | Link |
| Busco | 5.3.0 | MIT | link | link |
| BWA-mem2 | 2.2.2 | MIT | link | link |
| Canu | 2.2 | GPL 2.0 | link | link |
| ConfindR | 0.7.4 | MIT | link | link |
| DNAAPLER | 1.1.0 | MIT | link | |
| ECTyper | 2.0.0 | Apache 2.0 | link | |
| FastP | 0.24 | MIT | link | link |
| FastPlong | 0.4.1 | MIT | link | link |
| Flye | 2.9 | BSD 3 | link | link |
| Hifiasm | 0.25.0 | MIT | link | link |
| hAMRonization | 1.1.4 | LGPL 3.0 | link | |
| Homopolish | 0.4.1 | GPL 3.0 | link | link |
| Kaptive | 3.1.0 | GPL 3.0 | link | link |
| Lissero | 0.4.9 | GPL 3.0 | link | |
| Kraken2 | 2.1.2 | MIT | link | link |
| Medaka | 2.0.1 | ONT Public License | link | |
| Miniasm | 0.3 | MIT | github | |
| Minimap2 | 2.28 | MIT | link | link |
| MLST | 2.23.0 | GPL 2.0 | link | |
| Mob Suite | 3.1.8 | Apache 2.0 | link | link |
| MultiQC | 1.19 | GPL 3.0 | link | link |
| Mosdepth | 0.3.8 | MIT | link | |
| Necat | 0.0.1 | - | link | |
| Quast | 5.2.0 | Quast License | link | |
| Racon | 1.4.3 | MIT | link | link |
| Raven | 1.8.3 | MIT | link | |
| Plassembler | 1.8.1 | MIT | link | link |
| Polypolish | 0.6.0 | GPL 3.0 | link | link |
| Porechop_abi | 0.5.0 | GPL 3.0 | link | link |
| Prokka | 1.14.6 | GPL 3.0 | link | link |
| Samtools | 1.19 | MIT/Expat | link | link |
| SeqSero2 | 1.3.1 | GPL 2.0 | link | link |
| Shovill | 1.1.0 | GPL 3.0 | link | |
| Sistr | 1.1.1 | Apache 2.0 | link | |
| Sccmec | 1.2.0 | MIT | link | |
| Snippy | 4.6.0 | GPL 2.0 | link | |
| Sourmash | 4.8.4 | BDS 3 Clause | link | |
| Stecfinder | 1.1.0 | GPL 3.0 | link | |
| Tabix | 1.20 | MIT/Expat | link | link |
* This information comes without guarantees and should be independently verified if licensing is critical to your use case
Databases
| Package | Database | URL | License |
|---|---|---|---|
| Abricate | Ecoli_VF | link | Apache 2.0 |
| Abricate | Resfinder | link | Apache 2.0 |
| Abricate | EcOH | link | BSD |