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

[Jun Aruga <jaruga@redhat.com>]

Hi Andreas,

The 3 pipelines nf-core/nanoseq, nf-core/artic, nf-core/viralrecon I
shared are the most applicable (= the highest priority) to COVID-19
analysis. [1].
Now I share the additional 5 pipelines that are certainly relevant (=
the 2nd highest priority). [2]
This is the result of my interview in the nf-core Slack channel.

Could you check the packages situations in Debian?
Sorry I knew information about the 5 pipelines a few weeks ago. But I
took a time to summarize the list of the packages and email it.

* nf-core/scrnaseq (single cell)
* nf-core/smartseq2 (single cell)
* nf-core/sarek (whole-genome sequencing)
* nf-core/mag (meta-genomics)
* nf-core/bcellmagic (immune response)

https://github.com/nf-core/scrnaseq/blob/master/bin/scrape_software_versions.py
bustools
kallisto
multiqc
salmon
star

https://github.com/nf-core/smartseq2/blob/master/bin/scrape_software_versions.py
fastqc
multiqc

https://github.com/nf-core/sarek/blob/master/bin/scrape_software_versions.py
allelecount
ascat
bcftools
bwa
fastqc
freebayes
gatk
htslib
manta
multiqc
qualimap
r
samtools
snpeff
strelka
tiddit
vcftools
vep

https://github.com/nf-core/mag/blob/master/bin/scrape_software_versions.py
busco
cat
centrifuge
fastp
fastqc
filtlong
kraken2
megahit
metabat
multiqc
nanolyse
nanoplot
porechop
quast
spades

https://github.com/nf-core/bcellmagic/blob/master/bin/scrape_software_versions.py
changeo
fastqc
multiqc
muscle
presto
r
r-alakazam
r-shazam
r-tigger
vsearch


[1] nf-core Slack #covid19 channel
  https://nfcore.slack.com/archives/C0105J0J9T8/p1587480925053900
  > The pipelines you listed are the ones that are/will be most
applicable to COVID-19 analysis.
[2] nf-core Slack #covid19 channel
  https://nfcore.slack.com/archives/C0105J0J9T8/p1587498948095200
  > But the single cell pipelines could certainly be relevant. Also
sarek for whole-genome sequencing analysis, mag for metagenomics
analysis and bcellmagic for investigations into the immune response..

Thanks & Cheers,
Jun

-- 
Jun | He - His - Him