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BioMed Research International
/
2023
/
Article
/
Tab 1
/
Research Article
PHINDaccess Hackathons for COVID-19 and Host-Pathogen Interaction: Lessons Learned and Recommendations for Low- and Middle-Income Countries
Table 1
Summary of tools, databases and repository used during the hackathons.
Databases
GenBank (
https://www.ncbi.nlm.nih.gov/genbank
)
GISAID (
https://gisaid.org/
)
EBI/ENA (
https://www.ebi.ac.uk/ena/browser/home
)
PubMed (
https://pubmed.ncbi.nlm.nih.gov/
)
NCBI (
https://www.ncbi.nlm.nih.gov/
)
Tools
Communication tools
Slack
WhatsApp
Google Meet
Google Docs
Tools
Bioinformatics tools
FastQC
Trimmomatic
BWA
SPAdes
GATK4
Shiny, ShinyDashboard, visNetwork
RSeQC
Skewer
STAR
SALMON
DESeq2
EdgeR
Programming language
Perl
R
Shell
Python
Nextflow
Repository
GitHuB