nf-core / viralrecon Star 112 Code Issues Pull requests Assembly and intrahost/low-frequency variant calling for viral samples workflow nanopore virus pipeline nextflow assembly metagenomics variant-calling illumina oxford-nanopore amplicon viral ont nf-core long-read-sequencing artic covid-19 covid19 sars-cov-2 Updated Jul 3, 2024 Nextflow
nf-core / vipr Star 14 Code Issues Pull requests Assembly and intrahost / low-frequency variant calling for viral samples workflow virus pipeline nextflow metagenomics viruses variant-calling genome-assembly viral-ngs viral viral-genomics viral-metagenomics nf-core Updated Feb 12, 2020 Nextflow
ksumngs / v-met Star 3 Code Issues Pull requests A bare-bones, ridiculously simple metagenomics pipeline for viruses using Kraken 2 written in Nextflow. bioinformatics pipeline nextflow metagenomics viral kraken2 Updated Jan 15, 2024 Nextflow