Workflows
What is a Workflow?Filters
Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade
This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.
COVID-19: variation analysis on ARTIC PE data
The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...
Tests Assembly of bacterial paired-end short read data with generation of quality metrics and reports
Type: Galaxy
Creators: Abromics , Pierre Marin, Clea Siguret, abromics-consortium
Submitter: WorkflowHub Bot
Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation
Type: Galaxy
Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium
Submitter: WorkflowHub Bot
Pairwise alignment pipeline (genome to genome or reads to genome)
Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)
Scaffolding with Bionano
Scaffolding using Bionano optical map data
Inputs
- Bionano data [cmap]
- Estimated genome size [txt]
- Phased assembly generated by Hifiasm [gfa1]
Outputs
- Scaffolds
- Non-scaffolded contigs
- QC: Assembly statistics
- QC: Nx plot
- QC: Size plot
Purge Duplicate Contigs
Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)
Inputs
- Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
- Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
- Assembly to purge (e.g. hap1) ...
A pipeline for de novo transcriptome assembly of short reads from bulk RNA-seq
