This workflow performs subtyping and consensus sequence generation for batches of Illumina PE sequenced Influenza A isolates.

Workflow for variant analysis against a reference genome in GenBank format

Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade

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 ...

With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.

This pipeline is based on the work of the National Food Agency of Canada. Doi: 10.3389/fmicb.2020.00549

Snakemake workflow: dna-seq-varlociraptor

A ...

Call somatic, germline and LoH event variants from PE Illumina sequencing data obtained from matched pairs of tumor and normal tissue samples.

This workflow can be used with whole-genome and whole-exome sequencing data as input. For WES data, parts of the analysis can be restricted to the exome capture kits target regions by providing the optional "Regions of Interest" bed dataset.

The current version uses bwa-mem for read mapping and varscan somatic for variant calling and somatic status ...

PAIRED-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT THE MOST ADAPTED VADR MODEL for annotation (see vadr parameters).

SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).

SNP-Calling

GATK Variant calling pipeline for genomic data using Nextflow

Quickstart

Install Nextflow using the following command:

curl -s https://get.nextflow.io | bash

Index reference genome:

$ bwa index /path/to/reference/genome.fa

$ samtools faidx /path/to/reference/genome.fa

$ gatk CreateSequenceDictionary -R /path/to/genome.fa -O genome.dict

Launch the pipeline execution with ...