All Published Workflows

11 workflows that have been reviewed and published

gvclass
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gvclass: Taxonomic Classification of Giant Viruses and MAGs
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public

version 0.9.4 March 7, 2023 Giant viruses are abundant and diverse and frequently found in environmental microbiomes. gvclas...
Taxonomic classification fasttree prodigal Biopython BLAST CLICK Diamond hmmsearch (genouest) MAFFT API (EBI) Pandas Snakemake trimAl ete3 sklearn viral-genomics
Free
26
gezelvirus
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Gezelvirus Workflow: Studying a Polinton-like Virus in Phaeocystis globosa
public

public

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
Free
116
phaeocystis-viral-elements
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Phaeocystis Viral Elements Extraction Workflow for Polinton-like Virus Study
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public

The repository contains the bioinformatic workflow used for extraction of viral elements from Phaeocystis genomes for the...
MEGAHIT Bowtie 2 Cutadapt hmmsearch (genouest) pilon SAMtools seqkit Snakemake Trim_Galore viral-genomics
Free
34
vrapid
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vRAPID: Virus Reference-based Assembly and Identification Pipeline
public

public

The Virus Reference-based Assembly Pipeline and IDentification (vRAPID) tool runs the assembly, consensus calling and annotat...
FastQC kraken2 metaprokka Minimap2 MultiQC Picard pilon QualiMap shovill Snakemake viral-genomics
Free
13
insaflu_snakemake
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INSaFLU Snakemake
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public

curl -L https://github.com/con
ABRicate fasttree nanofilt nanostat tabix BCFtools BEDTools Biopython BWA Consensus FastQC FreeBayes iVar MAFFT API (EBI) Medaka Pandas Pangolin SAMtools seqret Snakemake snippy snpEff SPAdes Trimmomatic pysam PyYAML viral-genomics
Free
114
vipr
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Assembly and intrahost / low-frequency variant calling for viral samples
public

public

nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant ca...
BEDTools BWA FastQC Kraken lofreq SAMtools seqtk TADpole ViPR viral-genomics
Free
10
viralintegration
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Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
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public

nf-core/viralintegration is a bioinformatics best-practice analysis pipeline for the identification of viral integration e...
Chimera detection FastQC MultiQC Nextflow Pandas SAMtools STAR Trimmomatic viral-genomics
Free
23
extract-sra-viralrnaspades-pe
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Integration of SRA Data and Viral RNA-Seq Assembly using ViralRNAspades (Paired-End)
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public

extract 1 Id from SRA and assume it is PE as input to viralRNASpades.
fastq Galaxy SPAdes WorkflowHub viral-genomics
Free
0-view-complete-virus-identification
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Comprehensive view on plant virus classification.
public

public

Non-functional workflow to get a global view of possibilities for plant virus classification.
elastic-blast BLAST fastp FLASH Galaxy kraken2 Minimap2 NGSUtils Picard shovill WorkflowHub Plant biology viral-genomics
Free
virify
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detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies
public

public

VIRify VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contig...
FASTQ-illumina JSON raw sequence reads Sequencing quality control genetic variants prodigal virsorter BLAST chromoMap fastp FastQC hmmscan (EBI) Krona MashMap MultiQC SPAdes ggplot2 magrittr plotly viral-genomics
Free
48
nf-core-viralrecon
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Viralrecon - Bioinformatics analysis pipeline for low-frequency variant calling.
public

public

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
Free
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