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

[Steffen Möller <steffen_moeller@gmx.de>]

Hi Jun,

I concur that the nanopore associated workflows are of high priority.

On 09.05.20 22:10, Jun Aruga wrote:
> Hi Andreas,
>
> The 3 pipelines nf-core/nanoseq,

https://github.com/nf-core/nanoseq

Not the workflow is in Debian, but most of the tools it uses. Missing is
only the optional route embracing

https://github.com/lbcb-sci/graphmap2


> nf-core/artic,

Not in Debian, yet, but on its way on

https://salsa.debian.org/med-team/fieldbioinformatics

That was from during the Hackathon, no idea where this stands, now. No
ITP referenced.

> nf-core/viralrecon

That is the next-flow workflow, I understand - no, have not seen that, yet.

Nextflow itself causes some problems, if I get this right. Most tools
contributing to viralrecon are already in the distribution. Missing are

https://github.com/andersen-lab/ivar
http://snpeff.sourceforge.net/SnpEff.html
http://snpeff.sourceforge.net/SnpSift.html

http://cab.spbu.ru/software/meta-spades/
https://github.com/ekg/seqwish
https://github.com/BU-ISCIII/plasmidID

which are all in the de novo assembly section.

Concerning your list below I tend to think that Debian has them all with
a few exceptions (nanolyse, ...).

also listed above. Ubiquitous tools aside, like R or cat, they should be
listed on https://blends.debian.org/med/tasks/bio.

Does that help?

Best,

Steffen

> 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