Workflows
What is a Workflow?Filters
Phasing and imputation pipeline
Workflow for clinical metaproteomics database searching
The aim of this workflow is to handle the routine part of shotgun metagenomics data processing. The workflow is using the tools Kraken2 and Bracken for taxonomy classification and the KrakenTools to evaluate diversity metrics. This workflow was tested on Galaxy Australia. A How-to guide for the workflow can be found at: https://github.com/vmurigneu/kraken_howto_ga_workflows/blob/main/pages/taxonomy_kraken2_wf_guide.md
Article abstract
Permeability is an important molecular property in drug discovery, as it co-determines pharmacokinetics whenever a drug crosses the phospholipid bilayer, e.g., into the cell, in the gastrointestinal tract or across the blood-brain barrier. Many methods for the determination of permeability have been developed, including cell line assays, cell-free model systems like PAMPA mimicking, e.g., gastrointestinal epithelia or the skin, as well as the Black lipid membrane (BLM) and ...
Assembly Evaluation for ERGA-BGE Reports
One Assembly, Illumina WGS reads + HiC reads
The workflow requires the following:
- Species Taxonomy ID number
- NCBI Genome assembly accession code
- BUSCO Lineage
- WGS accurate reads accession code
- NCBI HiC reads accession code
The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and ...
Assembly Evaluation for ERGA-BGE Reports
One Assembly, HiFi WGS reads + HiC reads
The workflow requires the following:
- Species Taxonomy ID number
- NCBI Genome assembly accession code
- BUSCO Lineage
- WGS accurate reads accession code
- NCBI HiC reads accession code
The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and HiC ...
M6Allele Pipeline & M6Allele algorithm
Introduction
We have developed an algorithm called M6Allele for identifying allele-specific m6A modifications. To facilitate its usage by researchers, we have also encapsulated our analysis process into a pipeline. You can learn more about the pipeline and the algorithm's usage from the following two modules:
M6Allele Pipeline
PARAMETER INTRODUCTION
-g/--gtf
: ...
Nextflow Pipeline for DeepVariant
This repository contains a Nextflow pipeline for Google’s DeepVariant, optimised for execution on NCI Gadi.
Quickstart Guide
- Edit the
pipeline_params.yml
file to include:
samples
: a list of samples, where each sample includes the sample name, BAM file path (ensure corresponding .bai is in the same directory), path to an optional regions-of-interest BED file (set to''
if not required), and the model type.ref
: path to the reference FASTA (ensure ...
Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics, with updates November 2024.
Workflow inputs: reads as fastqsanger.gz (not fastq.gz), and primary assembly.fasta. (To change reads format: click on the pencil icon next to the file in the Galaxy history, then "Datatypes", then set "New type" as fastqsanger.gz). Note: the reads should be those that were used for the assembly (i.e., the filtered/cleaned reads), not the raw reads.
What it does: ...
Type: Galaxy
Creators: Kate Farquharson, Gareth Price, Simon Tang, Anna Syme
Submitters: Johan Gustafsson, Anna Syme