Idea wanted: What is the most key open source projects to fight COVID-19?
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
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