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nf-core/viralrecon
Edit

Assembly and intrahost/low-frequency variant calling for viral samples

ampliconarticassemblycovid-19covid19illuminalong-read-sequencingmetagenomicsnanoporeontoxford-nanoporesars-cov-2variant-callingviralvirus
This is the development version of the pipeline.
Launch development version https://github.com/nf-core/viralrecon
  • Introduction
  • Usage
  • Parameters
  • Output
  • Releases
    • 3.0.0
    • 2.6.0
    • 2.5
    • 2.4.1
    • 2.4
    • 2.3.1
    • 2.3
    • 2.2
    • 2.1
    • 2.0
    • 1.1.0
    • 1.0.0
    • dev
Introduction Usage Parameters Output Releases
  • 3.0.0
  • 2.6.0
  • 2.5
  • 2.4.1
  • 2.4
  • 2.3.1
  • 2.3
  • 2.2
  • 2.1
  • 2.0
  • 1.1.0
  • 1.0.0
  • dev
run with
See the docs on how to configure the Seqera Platform CLI.
  • nf-core
  • Nextflow
  • Seqera Platform
video introduction
Play
subscribers
116
stars
157
open issues
65
open PRs
8
last release
4 months ago
last update
4 months ago
included modules
abacasartic_guppyplexartic_minionbandage_imagebcftools_consensus and 53 more modules
included subworkflows
bam_markduplicates_picardbam_sort_stats_samtoolsbam_stats_samtoolsbam_variant_demix_boot_freyjafastq_align_bowtie2 and 3 more subworkflows
contributors
Github user drpatelh
Github user svarona
Github user saramonzon
Github user Joon-Klaps
Github user JoseEspinosa
Github user maxulysse
Github user heuermh
Github user antunderwood
Github user ggabernet
Github user Shettland
Github user jaimeozaez
Github user mashehu
Github user adamrtalbot
Github user ewels
Github user MiguelJulia
Github user stevekm
Github user AnnaNoren
Github user cjjossart
Github user tavareshugo
Github user CaparicaLeo
Github user FriederikeHanssen
Github user ErikaKvalem
Github user ktrns
Github user mattheww95
Github user jcurado-flomics
Github user KevinMenden
get help
Ask a question on Slack Open an issue on GitHub

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