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Merge pull request #7 from Kincekara/1.5.0-dev
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update readme
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Kincekara authored Feb 15, 2024
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Expand Up @@ -43,10 +43,10 @@ The following programs and tools are used in the C-BIRD pipeline.
| [QUAST](https://github.com/ablab/quast) | 5.2.0 | Genome assembly evaluation |
| [BUSCO](https://gitlab.com/ezlab/busco/-/tree/master) | 5.6.1 | Genomic data quality assesment |
| [mlst](https://github.com/tseemann/mlst) | 2.23.0 | MLST typing |
| [AMRFinderPlus](https://github.com/ncbi/amr) | 3.11.26 | AMR gene identification |
| [AMRFinderPlus](https://github.com/ncbi/amr) | 3.12.8 | AMR gene identification |
| [BLAST+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html)| 2.15.0 | Target gene search |
| [PlasmidFinder](https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/) | 2.1.6 | Plasmid detection |
| Cbird-Util | 1.0 | Individual summary report generation |
| Cbird-Util | 1.1 | Individual summary report generation |

## Outputs ##
In addition to outputs generated in each step by the specific programs, C-BIRD creates additional summary reports in HTML for each sample.
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