skim2rrna

skim2rrna is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of ribosomal genes 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 annotation ...

score-assemblies

A Snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina sequencing.

The workflow includes the following programs:

• pomoxis assess_assembly and assess_homopolymers
• dnadiff from the mummer package
• NucDiff
• QUAST
• BUSCO

...

ont-assembly-snake

A Snakemake wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data, using any combination of read filtering, assembly, long and short read polishing, and reference-based polishing.

Included programs

This project is about the automated quantification of wound healing in high-throughput microscopy scratch assays.

This is a Galaxy workflow for performing molecular dynamics simulations and analysis with flavivirus helicases in the Apo or unbound state. The associated input files can be found at: https://zenodo.org/records/7493015 The associated output files can be found at: https://zenodo.org/records/7850935

This is a Galaxy workflow for performing molecular dynamics simulations and analysis with coronavirus helicases bound to a ligand/drug molecule. The associated input files can be found at: https://zenodo.org/records/7492987. The associated output files can be found at: https://zenodo.org/records/7851000.

This is a Galaxy workflow for performing molecular dynamics simulations and analysis with coronavirus helicases in the Apo or unbound state. The associated input files can be found at: https://zenodo.org/records/7492987. The associated output files can be found at: https://zenodo.org/records/7851000.

This is a Galaxy workflow for performing molecular dynamics simulations and analysis with flavivirus helicases bound to a ligand/drug molecule. The associated input files can be found at: https://zenodo.org/records/7493015 The associated output files can be found at: https://zenodo.org/records/7850935

Protype demonstrator of a workflow reducing HESS and INTEGRAL/SPI-ACS data to common Light Curve format and combining the lightcurves into a multi-wavelength observation.

EBP-Nor Genome Assembly pipeline

This repository contains the EBP-Nor genome assembly pipeline. This pipeline is implemented in snakemake. This pipeline is developed to create haplotype-resolved genome assemblies from PacBio HiFi reads and HiC reads, and is primarly designed for diploid eukaryotic organisms. The pipeline is designed to work on a linux cluster with slurm as workload manager.

Requirements & Setup

Some software need to be configured/installed before the pipeline can be run ...