HiC contact map generation
Download RO-CrateHiC contact map generation
Snakemake pipeline for the generation of .pretext and .mcool files for visualisation of HiC contact maps with the softwares PretextView and HiGlass, respectively.
Prerequisites
This pipeine has been tested using Snakemake v7.32.4 and requires conda for installation of required tools. To run the pipline use the command:
snakemake --use-conda
There are provided a set of configuration and running scripts for exectution on a slurm queueing system. After configuring the cluster.json file run:
./run_cluster
Before starting
You need to create a temporary folder and specify the path in the config.yaml file. This should be able to hold the temporary files created when sorting the .pairsam file (100s of GB or even many TBs)
The path to the genome assemly must be given in the config.yaml.
The HiC reads should be paired and named as follows: Library_1.fastq.gz Library_2.fastq.gz. The pipeline can accept any number of paired HiC read files, but the naming must be consistent. The folder containing these files must be provided in the config.yaml.
Version History
Version 2 (latest) Created 29th Apr 2024 at 13:22 by Tom Brown
Frozen
Version-2fbee71d
Version 1 (earliest) Created 14th Mar 2024 at 09:50 by Tom Brown
Initial commit
Frozen
Version-1
e19ac74
Views: 1374 Downloads: 356
Created: 14th Mar 2024 at 09:50
Last updated: 14th Mar 2024 at 09:52
AttributionsNone
Collections
ERGA Assembly Snake...
Related items
https://orcid.org/0000-0001-8293-4816
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 ...
Teams: ERGA Assembly, ERGA Annotation
Web page: https://www.erga-biodiversity.eu/
Biodiversity Genomics Europe, funded by Horizon Europe call HORIZON-CL6-2021-BIODIV-01-01, aims at aligning the resources and research agendas of both DNA barcoding and reference genome generation, thus opening the door for a true quantum leap in biodiversity genomics research in Europe.
Despite ground-breaking developments in both DNA barcoding and full genome sequencing, there remains a critical need to develop and strengthen functioning communities of practice ...
Teams: Vertebrate Genomes Pipelines in Galaxy, Biodiversity Genomics Europe (general)
Web page: https://biodiversitygenomics.eu/
This is a general team for the BGE project for any members affiliated directly or indirectly with the BGE project.
To request joining this team, make sure sure your WorkflowHub institution matches one of the listed BGE partners.
Space: Biodiversity Genomics Europe (BGE)
Public web page: https://biodiversitygenomics.eu/
Start date: 1st Sep 2022
End date: 28th Feb 2026
A collection of workflows and pipelines developed as part of the ERGA consortium
Space: ERGA
Public web page: https://www.erga-biodiversity.eu/
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 ...
