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



Hi Jun,

thanks a lot for your input which is extremely helpful.

On Sat, May 09, 2020 at 10:10:33PM +0200, Jun Aruga wrote:
> 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.

Thanks for doing this.
 
> Could you check the packages situations in Debian?

Done below.  Every package without a remark is in Debian.  I gave
upstream URLs for those packages that are not yet touched and URLs on
salsa.debian.org for preliminary packaging stuff.  Sometimes I had
some additional comments from previous experience.

> 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.

That's fine.  We found other work to do meanwhile. ;-)
 
> * 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

    -> https://bustools.github.io/

> kallisto
> multiqc
> salmon
> star
   In Debian named rna-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

   -> https://github.com/cancerit/alleleCount

> ascat

   -> https://github.com/Crick-CancerGenomics/ascat

> bcftools
> bwa
> fastqc
> freebayes
> gatk

   -> https://salsa.debian.org/med-team/gatk

> htslib
> manta

   -> https://salsa.debian.org/med-team/manta

  May be somebody volunteers to ping upstream about a Python3 port here
   https://github.com/Illumina/manta/issues/180
  We can not get it into Debian before this is solved.

> multiqc
> qualimap

   -> https://salsa.debian.org/med-team/qualimap
   I once was pretty close to package this.  However it contains some binary
   JARs named bioinfo-commons-0.10.1.jar, bioinfo-ngs-0.1.0.jar, ...
   where the source just seems to be "lost".  See my discussion on the mailing list:

    https://groups.google.com/forum/#!msg/qualimap/KVJ8m5ZsAhU/O30pHTkADAAJ;context-place=searchin/qualimap/org.bioinfo

   If anybody has some idea where to find those sources that would be really
   helpful!

> r
> samtools
> snpeff

   -> https://salsa.debian.org/med-team/snpeff

> strelka

   -> https://github.com/Illumina/strelka/

> tiddit

   -> https://github.com/SciLifeLab/TIDDIT

> vcftools
> vep

   Please confirm that you mean
       https://github.com/Ensembl/ensembl-vep

 
> https://github.com/nf-core/mag/blob/master/bin/scrape_software_versions.py
> busco

   -> https://gitlab.com/ezlab/busco

> cat

   -> https://github.com/dutilh/CAT
   BTW, its not a good idea to name a tool like a pretty generid UNIX command

> centrifuge
> fastp
> fastqc
> filtlong
> kraken2
> megahit

  -> https://ftp-master.debian.org/new/megahit_1.2.9-1.html
     (just uploaded to new)

> metabat

  -> https://bitbucket.org/berkeleylab/metabat

> multiqc
> nanolyse

  -> https://pypi.org/project/NanoLyse/1.1.0/ (with version tag)
  -> Asked for release tags on https://github.com/wdecoster/nanolyse/issues/6

> nanoplot

  -> https://salsa.debian.org/med-team/nanoplot

> porechop
> quast

  -> https://salsa.debian.org/med-team/quast
  As I wrote in some other mail this itself has a lot of predepends
  that are included as binaries.

> spades
> 
> https://github.com/nf-core/bcellmagic/blob/master/bin/scrape_software_versions.py
> changeo
> fastqc
> multiqc
> muscle
> presto

   Binary package name is python3-presto

> r
> r-alakazam

  Binary package name is r-cran-alakazam

> r-shazam

  Binary package name is r-cran-shazam

> r-tigger

  Binary package name is r-cran-tigger

> vsearch


If anybody wants to work on one of the packages its probably helpful to
announce it here.
 
Kind regards and thanks again for your very helpful contribution

    Andreas.

 
> [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
> 
> 

-- 
http://fam-tille.de


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