Workflows
What is a Workflow?Filters
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
MGnify genomes catalogue pipeline
MGnify A pipeline to perform taxonomic and functional annotation and to generate a catalogue from a set of isolate and/or metagenome-assembled genomes (MAGs) using the workflow described in the following publication:
Gurbich TA, Almeida A, Beracochea M, Burdett T, Burgin J, Cochrane G, Raj S, Richardson L, Rogers AB, Sakharova E, Salazar GA and Finn RD. (2023) [MGnify Genomes: A Resource for Biome-specific Microbial Genome ...
Type: Nextflow
Creators: Ekaterina Sakharova, Tatiana Gurbich, Martin Beracochea
Submitter: Martin Beracochea
EnrichDO
EnrichDO is a double weighted iterative model by integrating the DO graph topology on a global scale. It was based on the latest annotations of the human genome with DO terms, and double weighted the annotated protein-coding genes. On one hand, to reinforce the saliency of direct gene-DO annotations, different initial weights were assigned to directly annotated genes and indirectly annotated genes, respectively. On the other hand, to detect locally most significant node between ...
This workflow will perform taxonomic and functional annotations using Unipept and statistical analysis using MSstatsTMT.
In proteomics research, verifying detected peptides is essential for ensuring data accuracy and biological relevance. This tutorial continues from the clinical metaproteomics discovery workflow, focusing on verifying identified microbial peptides using the PepQuery tool.
From metagenomes to peptides
Type: Nextflow
Creators: Sabrina Krakau, Leon Kuchenbecker and Till Englert
Submitter: WorkflowHub Bot