All Published Workflows
8 workflows that have been reviewed and published
RNA-seq Alignment and Counting Pipeline
This pipeline aims to provide a simple alignment tool for RNAseq data (without UMI). The fastq files are aligned on a referen...
Alignment and Annotation Pipeline for Klebsiella pneumoniae
MBB659 Final Project: Alignment and annotation pipeline for Klebsiella pneumoniae
Klebsiella pneumoniae is considered...
Fusarium Genome DNA-seq QC, Alignment, and Variant Calling Workflow Using Snakemake
Fusarium_workflow A basic snakemake file for QC, Alingment and Variant calling on DNAseq data of F.oxy.genome needs conda and...
Long Read Pipeline with Alignment and Dependency Information
The module consists of alignment .... In order to use this module, the following dependencies are required: Input data should...
Sentieon Tools for Alignment and Variant Analysis
The module consists of tools from Sentieon, including alignment, duplicate reads removal, indel realignment, recalibration ta...
Realignment Pipeline for Increased Reproducibility and Portability
This realignment pipeline is a reimplantation of the pipeline found at https://github.com/BrenKenna/data_processing. The orig...
Amplicon Sequencing snakemake workflow
AmpSeeker is a snakemake workflow for Amplicon Sequencing data analysis. The pipeline is a work in progress, however, it curr...
Purge duplicates from hifiasm assembly v1.0
Please see the Genome assembly with hifiasm on Galaxy Australia guide.
The workflow & the doc_guidelines template used ar...