README.md updated

iLivius · May 19, 2024 · 49465d5 · 49465d5
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-BacFluxL+ v1.1
+BacFluxL+ v1.1.1
 
 May 2024
 ```
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 - `10.annotation`: Based on long-read assembled, reoriented, error corrected contigs. Contains the following sub-directories:
     - **prokka**: Legacy annotation performed by [Prokka](https://github.com/vdejager/prokka) (v1.14.6).
-    - **bakta**: Accurate annotation outputted by [Bakta](https://github.com/oschwengers/bakta) (v1.9.1).
+    - **bakta**: Accurate annotation outputted by [Bakta](https://github.com/oschwengers/bakta) (v1.9.3).
     - **eggnog**: Functional annotation produced by [EggNOG](https://github.com/eggnogdb) mapper (v2.1.12).
-    - **antismash**: Secondary metabolites inferred by [antiSMASH](https://github.com/antismash/antismash) (v6.1.1).
+    - **antismash**: Secondary metabolites inferred by [antiSMASH](https://github.com/antismash/antismash) (v7.1.0).
 
 - `11.AMR`: Antimicrobial resistance features are investigated with two complementary approaches:
     - **AMR_mapping**: short reads filtered by [fastp](https://github.com/OpenGene/fastp) (v0.23.4) are mapped to the CARD database (v3.2.9.) using [BBMap](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/) (v39.06) with minimum identiy = 0.99. Mapping results are parsed and features with a covered length of at least 70% are reported in the `AMR legend` file.
@@ -380,7 +380,7 @@ The workflow output reflects the steps described in the [description](#descripti
     2. [QualiMap](http://qualimap.conesalab.org/) (v2.3)
     3. [Quast](https://github.com/ablab/quast) (v5.2.0)
     4. [Prokka](https://github.com/vdejager/prokka) (v1.14.6)
-    5. [Bakta](https://github.com/oschwengers/bakta) (v1.9.1)
+    5. [Bakta](https://github.com/oschwengers/bakta) (v1.9.3)
 
 ## Acknowledgements
 This work was supported by the [Austrian Science Fund (FWF)](https://www.fwf.ac.at/en/) [Project I6030-B].
@@ -391,7 +391,7 @@ Antonielli, L., Nagel, M., Sanchez Mejia, A., Koch, H., Trognitz, F., & Großkin
 ## References
 1. Alcock, B. P., Huynh, W., Chalil, R., Smith, K. W., Raphenya, A. R., Wlodarski, M. A., Edalatmand, A., Petkau, A., Syed, S. A., Tsang, K. K., Baker, S. J. C., Dave, M., McCarthy, M. C., Mukiri, K. M., Nasir, J. A., Golbon, B., Imtiaz, H., Jiang, X., Kaur, K., … McArthur, A. G. (2023). CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51(D1), D690–D699. https://doi.org/10.1093/nar/gkac920
 2. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 19(5), 455–477. https://doi.org/10.1089/cmb.2012.0021
-3. Blin, K., Shaw, S., Kloosterman, A. M., Charlop-Powers, Z., van Wezel, G. P., Medema, M. H., & Weber, T. (2021). antiSMASH 6.0: Improving cluster detection and comparison capabilities. Nucleic Acids Research, 49(W1), W29–W35. https://doi.org/10.1093/nar/gkab335
+3. Blin, K., Shaw, S., Augustijn, H. E., Reitz, Z. L., Biermann, F., Alanjary, M., Fetter, A., Terlouw, B. R., Metcalf, W. W., Helfrich, E. J. N., van Wezel, G. P., Medema, M. H., & Weber, T. (2023). antiSMASH 7.0: New and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Research, 51(W1), W46–W50. https://doi.org/10.1093/nar/gkad344
 4. Bouras, G., Grigson, S. R., Papudeshi, B., Mallawaarachchi, V., & Roach, M. J. (2024). Dnaapler: A tool to reorient circular microbial genomes. Journal of Open Source Software, 9(93), 5968. https://doi.org/10.21105/joss.05968
 5. Bushnell, B. (2014). BBMap: A Fast, Accurate, Splice-Aware Aligner. https://escholarship.org/uc/item/1h3515gn
 6. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10, 421. https://doi.org/10.1186/1471-2105-10-421