Top 6 genome-analysis open source projects
mccortex
De novo genome assembly and multisample variant calling
EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
TeamTeri
Genomics using open source tools, running on GCP or AWS
bacannot
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
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NextflowgroovyrDockerfilepythonshellpipelineannotationreproducible-researchvirulence-factorgenome-browsergenome-analysisrgivirulence-genesmobile-genetic-elementsbarrnapprophagesantimicrobial-genes-annotationmethylation-annotationko-annotationinsertion-sequencesgenomic-islands-predictionprophage-sequences-predictionphigarorrna-predictionWinnowmap
Long read / genome alignment software
PopGenome
An Efficient Swiss Army Knife for Population Genomic Analyses in R
1-6 of 6 genome-analysis projects