ERGA DataQC ONT v2505 (WF0)

Version 1

Welcome to the ERGA Space!

Here we collect, curate and develop pipelines to assemble and annotation reference-quality genomes for all eukaryotic life.

For Genome Assembly pipelines head to our Assembly Team

For Genome Annotation pipelines head to our Annotation Team

Development, discussions and issue tracking takes place in the ERGA github repo

If you would like to join ...

A collection of workflows and pipelines developed as part of the ERGA consortium

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be PacBio HiFi or ONT reads and Illumina 3-dimensional Chromatin Confirmation Capture (Hi-C) reads

Executing the workflows collection will output a scaffolded primary assembly and alternate contigs, with the complete QC analyses

Please run the workflows in order: WF0', WF1, WF2, WF3, WF4

'Notice there is one for HiFi, one for ONT, and one for Illumina (WGS or Hi-C). Run according to your data. ...

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

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