Colin Davenport's repositories
hardware_introduction
What scienfitic programmers must know about CPUs and RAM to write fast code.
masterBLASTer
A SLURM tool for performing parallel BLAST searches
singularity_scrna_app
READ ONLY A test environment for scrna_seq_apps
ampliseq
16S rRNA amplicon sequencing analysis workflow using QIIME2
ansible-galaxy-extras
Ansible roles to configure assorted compontents for an Ubuntu VM or container configured with https://github.com/galaxyproject/ansible-galaxy with production services including nginx, uwsgi, supervisor, protftp, and slurm.
ansible-galaxy-os
An Ansible role is for configuring the base operating system useful for running Galaxy.
assembly_polishing_racon_medaka
Slurm-pipeline for polishing assemblys with nanopore reads
awesome-microbes
List of computational resources for analyzing microbial sequencing data.
bionitio-rust
Demonstrating best practices for bioinformatics command line tools
blast-example
A basic blast pipeline using nextflow
CITE-seq-Count
A tool that allows to get UMI counts from a single cell protein assay
containerd
An open and reliable container runtime
GalaxyKickStart
Ansible playbooks for Galaxy Server deployment
genmap
GenMap - Fast and Exact Computation of Genome Mappability
gtf_last_exon_filter
A python script to filter and include the last exons of every transcript.
Heatmaps
Heatmap script for Wochenende output files
HOME
DMR Identification Tool
hpc-intro
Intro to HPC lesson materials
jbrowse-components
Monorepo with JBrowse 2 web, JBrowse 2 desktop, and more.
methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
nextflow
A DSL for data-driven computational pipelines
nf-co.re
Files for the main nf-core website >>>
Ratatosk
Hybrid error correction of long reads using colored de Bruijn graphs
scrnaseq_app
UNDER DEVELOPMENT: Shiny app for visualisation of scRNASeq data
we_config
conda config files for Wochenende
wtdbg2
Important update of wtdbg