GALOP - Genome Assembly using Long reads Pipeline

This repository contains an exact copy of the standard Genoscope long reads assembly pipeline.

At the moment, this is not intended for users to download as it uses grid submission commands that will only work at Genoscope. As time goes on, we intend to make this pipeline available to a broader audience. However, genome assembly and polishing commands are accessible in the lib/assembly.py and lib/polishing.py files.

galop.py -h 
Mandatory
...

skim2mito

skim2mito is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.

Contents

• Setup
• Example data
• Input
• Output
• Filtering contaminants
• [Assembly and ...

Assembly Evaluation for ERGA-BGE Reports

One Assembly, HiFi WGS reads + HiC reads

The workflow requires the following:

• Species Taxonomy ID number
• NCBI Genome assembly accession code
• BUSCO Lineage
• WGS accurate reads accession code
• NCBI HiC reads accession code

The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and HiC ...

Assembly Evaluation for ERGA-BGE Reports

One Assembly, Illumina WGS reads + HiC reads

The workflow requires the following:

• Species Taxonomy ID number
• NCBI Genome assembly accession code
• BUSCO Lineage
• WGS accurate reads accession code
• NCBI HiC reads accession code

The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and ...

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 ...

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