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Library curation BOLD
This repository contains scripts and synonymy data for pipelining the automated curation of BOLD data dumps in BCDM TSV ...
Type: Snakemake
Creators: Rutger Vos, Fabian Deister, Ben Price, Special thanks to Sujeevan Ratnasingham and the team at CBG for the creation of the BCDM data exchange format that this pipeline operates on
Submitter: Rutger Vos
HiC scaffolding pipeline
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
...
Purge dups
This snakemake pipeline is designed to be run using as input a contig-level genome and pacbio reads. This pipeline has been tested with snakemake v7.32.4. Raw long-read sequencing files and the input contig genome assembly must be given in the config.yaml file. To execute the workflow run:
snakemake --use-conda --cores N
Or configure the cluster.json and run using the ./run_cluster command
HiC 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 ...
Bactria: BarCode TRee Inference
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