Combined workflows for large genome assembly Version 1
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Run on usegalaxy.euCombined workflow for large genome assembly
The tutorial document for this workflow is here: https://doi.org/10.5281/zenodo.5655813
What it does: A workflow for genome assembly, containing subworkflows:
- Data QC
- Kmer counting
- Trim and filter reads
- Assembly with Flye
- Assembly polishing
- Assess genome quality
Inputs:
- long reads and short reads in fastq format
- reference genome for Quast
Outputs:
- Data information - QC, kmers
- Filtered, trimmed reads
- Genome assembly, assembly graph, stats
- Polished assembly, stats
- Quality metrics - Busco, Quast
Options
- Omit some steps - e.g. Data QC and kmer counting
- Replace a module with one using a different tool - e.g. change assembly tool
Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)
Steps
| ID | Name | Description |
|---|---|---|
| 5 | kmer counting - meryl | c0b5fbb61b12154d |
| 6 | Data QC | ae3b48869cad659b |
| 7 | Trim and filter reads - fastp | 2ed2445df255451a |
| 8 | Assembly with Flye | ec0fc1dbb6a13fe5 |
| 9 | Assembly polishing | 1fbcdce7d5823b15 |
| 10 | Assess genome quality | 9d0e6aba18484ea8 |
Version History
Version 1 (earliest) Created 8th Nov 2021 at 06:08 by Anna Syme
Added/updated 2 files
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Created: 8th Nov 2021 at 06:08
Last updated: 11th Nov 2021 at 03:37
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https://orcid.org/0000-0002-9906-0673
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia
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The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Space: Australian BioCommons
Public web page: https://www.biocommons.org.au/
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
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Space: Australian BioCommons
Public web page: https://usegalaxy.org.au/
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 ...
