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27 Collections visible to you, out of a total of 27

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 a scaffolded primary assembliy and alternate contigs, with 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: Diego De Panis

Number of items: 6

Tags: Not specified

EuCanImage FHIR ETL Implementation

This repository contains the ETL implementation for EuCanImage, encouraging semantic interoperability of the clinical data obtained in the studies by transforming it into a machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create the dictionaries following a FHIR compliant structure.

Maintainers: Aldar Cabrelles

Number of items: 5

Tags: Not specified

Pipelines used by the genomes assembly teams part of the Biodiversity Genomics Europe project

https://biodiversitygenomics.eu/

Maintainers: Tom Brown

Number of items: 2

Tags: Assembly, Genomics, Biodiversity

Collection of Galaxy workflows for generating results used for creating ERGA-BGE Reports

For a given genome, two workflows should be run: the assembly evaluation (ASM analyses), and the annotation evaluation (ANNOT analyses)

Depending on the kind of data used for the genome assembly, you should choose HiFi or ONT (Illumina) workflows for ASM analyses

Maintainers: Diego De Panis

Number of items: 3

Tags: Genomics, QC, Genome assembly

Workflows developed by or used by BY-COVID project.

Maintainers: Stian Soiland-Reyes

Number of items: 3

Tags: Not specified

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

Maintainers: Anna Syme

Number of items: 7

Tags: TSI-annotation

eDNA Protocols for BGE (Biodiversity Genomics Europe) Work package 6, task 6.2

Maintainers: Cátia Chaves

Number of items: 2

Tags: Not specified

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

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