Authors: V. Murigneux, L. W. Roberts, B. M. Forde, M. D. Phan, N. T. K. Nhu, A. D. Irwin, P. N. A. Harris, D. L. Paterson, M. A. Schembri, D. M. Whiley, S. A. Beatson
Date Published: 25th Jun 2021
Publication Type: Journal
PubMed ID: 34172000
Citation: BMC Genomics. 2021 Jun 25;22(1):474. doi: 10.1186/s12864-021-07767-z.
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
Workflow (hybrid) metagenomic assembly and binning + GEMs
Accepts both Illumina and Long reads (ONT/PacBio)
Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
Workflow LongRead Quality: https://workflowhub.eu/workflows/337
Kraken2 taxonomic classification of FASTQ reads
QUAST (Assembly quality report)
Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)
- DAS Tool
- CheckM ...
Workflow for LongRead Quality Control and Filtering
- NanoPlot (read quality control) before and after filtering
- Filtlong (read trimming)
- Kraken2 taxonomic read classification before and after filtering
- Minimap2 read filtering based on given references
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here: https://gitlab.com/m-unlock/cwl/workflows
**How to setup and use an UNLOCK ...
Shotgun Metagenomics Analysis
Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!
These scripts have been written ...
General recommendations for using
Please see the
Genome assembly with hifiasm on Galaxy Australia guide.
The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian ...
Flashlite-Trinity contains two workflows that run Trinity on the University of Queensland's HPC, Flashlite. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. Users can run Flashlite-Trinity on single samples, or smaller samples requiring <500Gb ...
Description: Trinity @ NCI-Gadi contains a staged Trinity workflow that can be run on the National Computational Infrastructure’s (NCI) Gadi supercomputer. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. ...
microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.
To build microPIPE we evaluated the performance of several tools at each step of bacterial genome assembly, including basecalling, assembly, and polishing. Results at each step were validated using the high-quality ST131 Escherichia coli strain EC958 (GenBank: HG941718.1). After appraisal of each step, we selected the best combination of ...
A porting of the Trinity RNA assembly pipeline, https://trinityrnaseq.github.io, that uses Nextflow to handle the underlying sub-tasks. This enables additional capabilities to better use HPC resources, such as packing of tasks to fill up nodes and use of node-local disks to improve I/O. By design, the pipeline separates the workflow logic (main file) and the cluster-specific configuration (config files), improving portability.
Based on a pipeline by Sydney Informatics Hub: ...
Virus genome assembly with Unicycler and Spades, The 2 assemblers works in parallel. The graph visualization is made with Bandage. workflow git repository : https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/master/Assembly/workflow/assembly-wf-virus.cwl Based on https://github.com/galaxyproject/SARS-CoV-2/blob/master/genomics/2-Assembly/as_wf.png
Type: Common Workflow Language
Submitter: francois moreews