All Published Workflows
11 workflows that have been reviewed and published
gvclass: Taxonomic Classification of Giant Viruses and MAGs
version 0.9.4 March 7, 2023 Giant viruses are abundant and diverse and frequently found in environmental microbiomes. gvclas...
Gezelvirus Workflow: Studying a Polinton-like Virus in Phaeocystis globosa
The repository contains the bioinformatic workflow used in the paper Roitman et al (2023) "Infection cycle and phylogeny of a...
prodigal
raxml-ng
vcontact2
APE
Biopython
BLAST
FiMO
GAPPA
gffcompare
gffread
ggseqlogo
ggtree
HHblits
hmmalign (genouest)
hmmbuild (genouest)
hmmscan (EBI)
hmmsearch (genouest)
MAFFT API (EBI)
MCL
MEME
metaprokka
MMseqs
Pandas
seqkit
seqret
Snakemake
subSeq
treeio
trimAl
cowplot
dplyr
ggforce
ggplot2
ggraph
igraph
phangorn
phytools
scatterpie
stringr
tibble
tidyr
tidyverse
XML
epang
lxml
six
viral-genomics
Phaeocystis Viral Elements Extraction Workflow for Polinton-like Virus Study
The repository contains the bioinformatic workflow used for extraction of viral elements from Phaeocystis genomes for the...
vRAPID: Virus Reference-based Assembly and Identification Pipeline
The Virus Reference-based Assembly Pipeline and IDentification (vRAPID) tool runs the assembly, consensus calling and annotat...
Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
nf-core/viralintegration is a bioinformatics best-practice analysis pipeline for the identification of viral integration e...
Integration of SRA Data and Viral RNA-Seq Assembly using ViralRNAspades (Paired-End)
extract 1 Id from SRA and assume it is PE as input to viralRNASpades.
Comprehensive view on plant virus classification.
Non-functional workflow to get a global view of possibilities for plant virus classification.
detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies
VIRify VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contig...
Viralrecon - Bioinformatics analysis pipeline for low-frequency variant calling.
nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intrahost/low-frequency variant calli...
Variant calling
assembly_improvement
artic
asciigenome
nextclade
tabix
Bandage
BCFtools
BEDTools
BLAST
Bowtie 2
Consensus
Cutadapt
fastp
FastQC
iVar
kraken2
Minia
mosdepth
MultiQC
NanoPlot
Nextflow
Pangolin
Picard
PlasmidID
QUAST
SAMtools
snpEff
SnpSift
SPAdes
Unicycler
Vcflib
pycoQC
Sequence analysis
viral-genomics