Watching COVID19 Virtual BioHackathon 2020 kick-off [1] and wrap-up [2] videos, I was thinking about this question.
What are the most key open source projects (or packages) that we need to care to maintain to fight COVID-19? "key" means the packages that we care more about than other packages. Sorry for the ambiguous question. I am curious and want to be concious about the priorities. Well, it's a broader topic. There are several factors such as Sequencing, Machine Learning, Graph, Workflow and etc in it. I shared the 3 nf-core pipelines nf-core/nanoseq, nf-core/artic, nf-core/viralrecon in the email thread: Subject https://github.com/nf-core/covid19 - nextflow pipeline . And the following are the used software in each pipeline. In my option, the packages written in compiling language such as C, C++ and taking long time to compile are the "key" packages. Because users can still run the script language software without deb package, and users can compile software that is easy to compile by themselves. And the essential function's software is also the key. In this case, that is sequencing aligner. So, the key packages are bowite2, minimap2, bwa in the list of the pipelines. And simde is used to support the packages on multiple CPU architctures [3]. So, the most key packages that we care about to fight COVID-19 are in order to the priority. 1. simde 2. bowtie2 (build time is long. It's relatively hard to compile it). 3. minimap2 4. bwa That's my observation. So, do you have any ideas or observations about the question? I would like to hear. Thank you. ## Used software in each pipeline. https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py guppy qcat pycoQC NanoPlot' FastQC GraphMap2 minimap2 Samtools BEDTools MultiQC' https://github.com/nf-core/artic/blob/dev/bin/scrape_software_versions.py FastQC NanoPlot BWA minimap2 Samtools BEDTools MultiQC https://github.com/nf-core/viralrecon/blob/dev/bin/scrape_software_versions.py parallel-fastq-dump FastQC fastp Bowtie 2 Samtools BEDTools Picard iVar VarScan 2 SnpEff SnpSift' BCFTools Cutadapt Kraken2 SPAdes Unicycler minia Minimap2 vg BLAST ABACAS QUAST R MultiQC' [1] https://youtu.be/x-QTP5Z_WIU [2] https://youtu.be/g5cQk8jIMwo [3] https://wiki.debian.org/SIMDEverywhere -- Jun | He - His - Him
