updated citations

CITATIONS.md

@@ -10,11 +10,84 @@
 
 ## Pipeline tools
 
+- [Abricate](https://github.com/tseemann/abricate)
+  > Seemann T, Abricate, Github https://github.com/tseemann/abricate
+
+- [Bakta](https://github.com/oschwengers/bakta#citation)
+  > Schwengers O., Jelonek L., Dieckmann M. A., Beyvers S., Blom J., Goesmann A. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11). https://doi.org/10.1099/mgen.0.000685
+
+- [Bandage](https://github.com/rrwick/Bandage.git)
+  > Wick R.R., Schultz M.B., Zobel J. & Holt K.E. (2015). Bandage: interactive visualisation of de novo genome assemblies. Bioinformatics, 31(20), 3350-3352.
+
+- [CheckM](https://github.com/Ecogenomics/CheckM)
+  > Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2014. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25: 1043-1055.
+
+- [ECTyper](https://github.com/phac-nml/ecoli_serotyping)
+  > Bessonov K, Laing C, Robertson J, Yong I, Ziebell K, Gannon VPJ, Nichani A, Arya G, Nash JHE, Christianson S. ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data. Microb Genom. 2021 Dec;7(12):000728. doi: 10.1099/mgen.0.000728. PMID: 34860150; PMCID: PMC8767331.
+
+- [FastP](https://doi.org/10.1093/bioinformatics/bty560)
+  > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884-i890, https://doi.org/10.1093/bioinformatics/bty560
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
+- [Flye](https://github.com/fenderglass/Flye)
+  > Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P. L. Smith and Pavel A. Pevzner "metaFlye: scalable long-read metagenome assembly using repeat graphs", Nature Methods, 2020 doi:s41592-020-00971-x
+
+- [GTDB](https://gtdb.ecogenomic.org/)
+  > Donovan H Parks, Maria Chuvochina, Christian Rinke, Aaron J Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz, GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D785–D794, https://doi.org/10.1093/nar/gkab776
+
+- [Kleborate](https://github.com/klebgenomics/Kleborate)
+  > Lam, MMC. et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications (2021)
+
+- [Kraken2](https://github.com/DerrickWood/kraken2)
+  > Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0
+
+- [LisSero](https://github.com/MDU-PHL/LisSero)
+  > Doumith et al. Differentiation of the major Listeria monocytogenes serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22
+
+- [Mash](https://github.com/marbl/Mash)
+  > Mash: fast genome and metagenome distance estimation using MinHash. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x.
+
+- [Medaka](https://github.com/nanoporetech/medaka)
+
+- [Minimap2](https://github.com/lh3/minimap2)
+  > Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574. doi:10.1093/bioinformatics/btab705
+
+- [mlst](https://github.com/tseemann/mlst)
+  > Seemann T, mlst Github https://github.com/tseemann/mlst
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [Pilon](https://github.com/broadinstitute/pilon)
+  > Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young, Ashlee M. Earl (2014) Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9(11): e112963. doi:10.1371/journal.pone.0112963
+
+- [Quast](https://github.com/ablab/quast)
+  > Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich, Versatile genome assembly evaluation with QUAST-LG, Bioinformatics (2018) 34 (13): i142-i150. doi: 10.1093/bioinformatics/bty266 First published online: June 27, 2018
+
+- [Racon](https://github.com/isovic/racon)
+  > Vaser R, Sović I, Nagarajan N, Šikić M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017 May;27(5):737-746. doi: 10.1101/gr.214270.116. Epub 2017 Jan 18. PMID: 28100585; PMCID: PMC5411768.
+
+- [Samtools](https://github.com/samtools/samtools)
+  > Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
+
+- [Seqtk](https://github.com/lh3/seqtk.git)
+
+- [Shigatyper](https://github.com/CFSAN-Biostatistics/shigatyper)
+  > Wu Y, Lau HK, Lee T, Lau DK, Payne J In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification. Applied and Environmental Microbiology, 85(7). (2019)
+
+- [Sistr](https://github.com/phac-nml/sistr_cmd)
+  > The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
+
+- [Spades](https://github.com/ablab/spades)
+  > Bankevich A., Nurk S., Antipov D., Gurevich A., Dvorkin M., Kulikov A. S., Lesin V., Nikolenko S., Pham S., Prjibelski A., Pyshkin A., Sirotkin A., Vyahhi N., Tesler G., Alekseyev M. A., Pevzner P. A. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 2012
+
+- [Spatyper](https://github.com/HCGB-IGTP/spaTyper)
+  > Jose Francisco Sanchez-Herrero, & mjsull. (2020). spaTyper: Staphylococcal protein A (spa) characterization pipeline (v0.3.1). Zenodo. https://doi.org/10.5281/zenodo.4063625
+
+- [Unicycler](https://github.com/rrwick/Unicycler)
+  > Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13(6): e1005595. https://doi.org/10.1371/journal.pcbi.1005595
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)