Collections

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads

Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses

Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4

This collection houses some scanpy-based scRNAseq workflows on galaxy Australia.

The aim of these workflows is to handle the routine ‘boring’ part of single cell RNAseq data processing. It will produces an ‘AnnData’ object, which can then be used as a base for downstream analysis – either within galaxy or outside of it. AnnData is a standard format used by the ‘scanpy’ python package.

These workflows represent just one way of processing data for a ‘typical’ scRNAseq experiment – there are many ...

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

This is a general collection of workflows used by or developed by members of the BGE project.

A set of generic and automatic workflows designed to: 

• Run on-the-fly and unattended.

• Maintain robust stability for a wide range of samples.

• Covers steps from movies to CTF estimation (for the moment).

• Monitor the acquisition process and provide user feedback.

• Comprise three proposed workflows, each with an additional layer of complexity.

Collection of workflows exploring data in the Image Data Resource (IDR).

This ARDC and BioCommons sponsored project delivers a key component of BioCommon’s vision for an ecosystem of platforms providing researchers with sophisticated data analysis and digital asset stewardship capabilities. The Bring Your Own Data (BYOD) Platform (https://www.biocommons.org.au/byod-expansion) has enabled highly accessible, highly available, highly scalable analysis and data sharing capabilities for the benefit of life science researchers nationally.

**This WorkflowHub collection ...

The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database.

TronFlow is an open source collection of computational workflows originally conceived for tumor-normal somatic variant calling over whole exome data and the manipulation of BAM and VCF files with the aim of having comparable and analysis-ready data. Over time, we have extended it to germline variant calling, copy numbers and other related technologies and analyses.

Its modular architecture covers different analytical and methodological use cases that allow analysing FASTQ files into analysis-ready ...