HiC scaffolding pipeline
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Snakemake pipeline for scaffolding of a genome using HiC reads using yahs.
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 --cores N
where N is number of cores to use. 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 21st Jun 2024 at 10:42 by Tom Brown
Add cluster json for execution on slurm
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Version 1 (earliest) Created 16th Mar 2024 at 09:01 by Tom Brown
Initial commit
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https://orcid.org/0000-0001-8293-4816
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A collection of workflows and pipelines developed as part of the ERGA consortium
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This is an inclusive collection of workflows related to biodiversity and ecology (especially non-microbial). A big portion covers genome assembly of newly-sequenced species, using long reads (ONT or PacBio HiFi), possibly complemented by chromosome capture (typically HiC) for scaffolding, or/and by short reads (typically Illumina). It also aims at collating workflows related to ecology, biodiversity, biogeography, natural history, and related scientific areas, across the whole WorkflowHub and ...
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Collection of workflows designed to assembled a set of PacBio HiFi and Illumina HiC reads into a chromosome-scale de-novo assembly.
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