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CDCgov / SARS-CoV-2_Sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
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How do I cite the Utah DoH ARTIC/Illumina Bioinformatic Workflow (Erin Young/Kelly Oakeson)? #41

Closed fhsantanna closed 3 years ago

fhsantanna commented 3 years ago

I have utilized the Utah DoH ARTIC/Illumina Bioinformatic Workflow (Erin Young/Kelly Oakeson) for genome assembly. How do I cite this protocol?

kapsakcj commented 3 years ago

CC @erinyoung

dmaccannell commented 3 years ago

I, uh... need to get better at updating and triaging issues.

erinyoung commented 3 years ago

Sorry! Didn't realize this question was being asked.

Are we working on a manuscript? Not really, so there's no specific paper to cite for the workflow. You'll want to include the github web address and version number.

The workflow, however, heavily uses ivar (https://pubmed.ncbi.nlm.nih.gov/30621750/), bwa (https://pubmed.ncbi.nlm.nih.gov/19451168/), samtools (https://pubmed.ncbi.nlm.nih.gov/33590861/ perhaps?), and nextflow (https://www.nature.com/articles/nbt.3820.epdf). It would be nice to get those creators the citations that they need.