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
