[covid-19] A relevant software mentioned during today's BH meeting (consider packaging)

[Liubov Chuprikova <chuprikovalv@gmail.com>]

Hi everyone,

I am going to share lists of packages/workflows that were mentioned during the "Kickoff" opening video conference today. Those are possible candidates for us to work on or to continue working on (if already in Debian):

• R package for the data collated by Johns Hopkins: https://github.com/rOpenStats/COVID19
• CHIME: COVID-19 Hospital Impact Model for Epidemics: https://penn-chime.phl.io
• COVID-19 Scenario simulator: https://github.com/neherlab/covid19_scenarios 
• The ARTIC Network: https://github.com/artic-network. I've seen, Porechop and Nanopolish are already in Debian. Maybe, Rampart is another possible candidate to package.
• R wrapper around the COVID Tracking Project API: https://github.com/aedobbyn/covid19us
  

Pipelines/Workflows:

• https://artic.network/ncov-2019 -- contains some bioinformatics protocols and datasets
  
• https://github.com/BU-ISCIII/SARS-Cov2_analysis/wiki/Analysis-pipelines
  
• Galaxy workflows: https://covid19.galaxyproject.org/genomics/ -- really nice and well structured, in my opinion
• Nexstrain workflows: https://github.com/nextstrain/ncov
• https://github.com/nf-core/viralrecon
  
• https://github.com/connor-lab/ncov2019-artic-nf
  

I also tried to filter out COVID19-related data resources. But, if someone needs it, there are, for example, wiki pages of `Bio statistics` and `Covid 19 Phylogeny` Topics (https://github.com/virtual-biohackathons/covid-19-bh20/wiki) with a lot of links to datasets.

I also mined a bit for some other viral genomics/epidemiology related software, that is not in Debian. These are not directly related to COVID19, but, I think, they deserve our attention:

• https://github.com/HaploConduct/HaploConduct -- Haplotype-aware genome assembly toolkit. HaploConduct consists of two methods: SAVAGE (Strain Aware VirAl GEnome assembly) and POLYTE (POLYploid genome fitTEr)
• https://github.com/chanzuckerberg/idseq-dag -- Pipeline engine for IDseq (Infectious Disease Sequencing Platform)
• https://github.com/chanzuckerberg/idseq-bench -- IDseq infectious disease benchmarking tools
• https://github.com/rcs333/VAPiD -- Viral Annotation and Identification Pipeline
• https://github.com/DennisSchmitz/Jovian -- Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail.
• https://github.com/viromelab/tracespipe -- Reconstruction and analysis of viral and human-host genomes at multi-organ level
• https://github.com/babinyurii/recan -- genetic distance plotting for recombination events analysis
• https://wupathlabs.wustl.edu/virusseeker/ -- a computational pipeline for virus discovery and virome composition analysis
• https://github.com/kentnf/VirusDetect -- an automated pipeline for efficient virus discovery using deep sequencing of small RNAs (Licence - ?)
• https://github.com/keylabivdc/VIP -- Virus Identification Pipeline (Licence - ?)
• https://github.com/ICBI/viGEN/ -- a bioinformatics pipeline for the exploration of viral RNA in human NGS data (Licence - ?)

I hope, it helps someone of you, especially newcomers, to choose a candidate for packaging.

I wish you all a productive week and hope to be able to contribute as well!

Regards,

Liubov