Workflows

Communication:

(@edawson says: I can host Zoom meetings and am happy to communicate by Telegram or Slack)

Projects:

Proposal: Cloud-based bioinformatics analysis (WDL + GCP) + accelerated pangenomic workflows (@edawson)

(links?)

Workflows:

connor-lab/ncov2019-artic-nf

https://github.com/connor-lab/ncov2019-artic-nf

A Nextflow pipeline that automates the ARTIC network nCoV-2019 novel coronavirus bioinformatics protocol. Supports barcoded and non-barcoded Nanopore data. Uses Nextflow DSLv2.

(todo: citation?)

galaxyproject/SARS-CoV-2

https://github.com/galaxyproject/SARS-CoV-2

Initial analysis of COVID-19 data using Galaxy, BioConda and public research infrastructure (XSEDE, de.NBI-cloud, ARDC cloud). Supports Illumina and Nanopore data.

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics

usegalaxy.org, usegalaxy.eu, usegalaxy.org.au, usegalaxy.be and hyphy.org development teams, Anton Nekrutenko, Sergei L Kosakovsky Pond.

bioRxiv 2020.02.21.959973; doi: 10.1101/2020.02.21.959973

nf-core/covid19

https://github.com/nf-core/covid19

In discussion whether to adapt the ARTIC network or Galaxy workflows or some or all of both to a new workflow. Aspires to become part of nf-core, a community effort to collect a curated set of analysis pipelines built using Nextflow.

Project communication for nf-core/covid19 is currently focused on Slack (you can join with this invite).

INSaFLU/INSaFLU

https://github.com/INSaFLU/INSaFLU

INSaFLU (“INSide the FLU”) is an influenza-oriented bioinformatics free web-based platform for an effective and timely whole-genome-sequencing-based influenza laboratory surveillance. Author states this online platform can also run for COVID-19.

INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance

Borges V, Pinheiro M et al.

Genome Medicine (2018) 10:46s; doi: 10.1186/s13073-018-0555-0

BU-ISCIII

Workflows for analyzing Illumina data both using amplicons and metagenomics approaches. Viral genome reconstruction and low frequency variants and annotation of both SNPs and INDELs. Uses Nextflow as DSL. Two different approaches using de novo assembly and mapping.

https://github.com/BU-ISCIII/SARS_Cov2_consensus-nf https://github.com/BU-ISCIII/SARS_Cov2_assembly-nf

Resources:

Participants:

• Eric Dawson
• Michael Heuer
• Rutger Vos (maybe, if using nextstrain)
• Stian Soiland-Reyes
• Tazro Ohta
• René Xavier (PhD candidate in Applied Genomics & Bioinformatics, limited skill set but eager to be of assistance!)
• Sara Monzón