Hiya, On Sun, 5 Apr 2020 at 23:05, Liubov Chuprikova <chuprikov...@gmail.com> wrote:
> 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 - ?) > > Thanks for the good work. To make this more organized and to avoid double work, I have created a wiki page here[1]. I would request all to add their name against the package when they start working on it, and tick the checkbox once done. [1]: https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work Best, Nilesh
