acknowledgements.md

Contributors and acknowledgements

Created by

    Aine O'Toole & Verity Hill       
            Rambaut Group              
        Edinburgh University   

Contributors

    Ben Jackson         gofasta       
    JT McCrone          clusterfunk     
    Stefan Rooke        local map 
    Andrew Rambaut      jclusterfunk 

Funding

                                            
                ARTIC Network               
    Wellcome Trust Collaborators Award      
                206298/Z/17/Z               
                                            
        COVID-19 Genomics UK Consortium     
    UK Department of Health and Social Care 
        UK Research and Innovation          
                                            
                ReservoirDOCs               
European Research Council Consolidator Grant
                ERC-2016-COG                
                                            

Acknowledgements

We thank the following for helpful suggestions, 
comments, beta-testing, feature requests and
patience.                
                                        
    :nickloman:         :mattloose:     
    :mattbashton:       :tomconnor:     
    :rebeccadewar:      :martinmchugh:    
    :richardmyers:      :meerachand:    
    :samnicholls:       :radpoplawski:   
    :davidaanensen:     :benlindsey:    
    :jeffbarrett:       :derekfairley:   
    :josephhughes:      :davidrobertson:  
    :richardorton:      :mattholden:
    :ulfschaefer:       :nataliegroves:   
    :nikosmanesis:      :jaynaraghwani:   


We acknowledge the hard work from all members of the 
COG-UK consortium that has gone into generating the 
data used by `civet`.

We acknowledge the hard work and open-science of the 
individual research labs and public health bodies 
that have made their genome data accessible on GISAID. 
A detailed table of acknowledgements for the SARS-CoV-2
genome sequences used to build this lineage system is 
hosted [here](https://github.com/cov-ert/clusterfunk))

References

baltic

Gytic Dudas

minimap2

Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, 15 September 2018, Pages 3094–3100, https://doi.org/10.1093/bioinformatics/bty191

iqtree

L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.. Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300

D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk, Olivier Gascuel, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, Volume 59, Issue 3, May 2010, Pages 307–321, https://doi.org/10.1093/sysbio/syq010

snakemake

Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.

Software versions

    - python=3.6
    - snakemake-minimal=5.13 
    - iqtree=1.6.12
    - minimap2=2.17-r941
    - pandas==1.1.0
    - pytools=2020.1
    - dendropy=4.4.0
    - tabulate=0.8.7