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20 Collections visible to you, out of a total of 21

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 ...

Maintainers: Tom Brown, Diego De Panis, ERGA

Number of items: 3

Tags: Genome assembly

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

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, ...

Maintainers: Björn Grüning

Number of items: 6

Tags: covid-19, Galaxy

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 ...

Maintainers: Genís Bayarri, Adam Hospital

Number of items: 17

Tags: Bioinformatics, BioBB

Collection of workflows used or developed by the EuroScienceGateway project.

Maintainers: Stian Soiland-Reyes, Paul De Geest

Number of items: 10

Tags: Not specified

Workflows developed by or used by BY-COVID project.

Maintainers: Stian Soiland-Reyes

Number of items: 0

Tags: Not specified

This collection contains all the pipelines and methods used to generate reference genome assemblies in the Tree of Life department of the Sanger institute

Maintainers: Matthieu Muffato

Number of items: 1

Tags: Not specified

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

Maintainers: Tom Brown, Diego De Panis

Number of items: 6

Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, HiFi, Hi-C

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 ...

Maintainers: Sarah Williams

Number of items: 8

Tags: Not specified

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