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Workflows developed by or used by BY-COVID project.
This is part of a series of workflows to annotate a genome, tagged with TSI-annotation
.
These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.
The workflows can be run in this order:
- Repeat masking
- RNAseq QC and read trimming
- Find transcripts
- Combine transcripts
- Extract transcripts
- Convert formats
- Fgenesh annotation
eDNA Protocols for BGE (Biodiversity Genomics Europe) Work package 6, task 6.2
Collection of workflows designed to assembled a set of PacBio HiFi and Illumina HiC reads into a chromosome-scale de-novo assembly.
Development versions of these pipelines can be found in the ERGA github and any questions or queries can be raised on the ERGA Discussions Channel
Want to find out more about the work done by ERGA? Become a member ...
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4
Maintainers: Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4
Maintainers: Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C
Solutions to the exercises on the Workflow Provenance part, during January 2024 COMPSs Tutorial.
The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, ...
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...
Collection of workflows used or developed by the EuroScienceGateway project.