Colin Davenport's repositories
awesome-pangenomes
A list of software for pangenomics
guppy_on_slurm
Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
rs_demultiplex
Simple demultiplexing of FASTQ, one oligo (barcode) at a time
blacklister
Improve your metagenomic reference sequence: Simple adapter and contamination FASTA masking using bowtie2 and bedtools
jbrowse2_utils
Bash scripts for writing assemblies and tracks to JBrowse2 https://jbrowse.org/jb2/
rusty_samplesheet
Very simple Illumina SampleSheet validation in Rust. Make your biologists check their own custom SampleSheets! Can be compiled for Windows users.
wochenende_manuscript
Code accompanying the Wochenende metagenomics analyzer manuscript
awesome-HiC
Awesome list of HiC data analysing tools
awesome-nanopore
A curated list of awesome nanopore analysis tools.
awesome-nextflow
A curated list of nextflow based pipelines
DGE
Nextflow pipeline that runs DESeq2 on data processed with the nextflow RNAseq pipeline
differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
docker-genomic-analysis
Basic docker image for ad-hoc genomic analyses
genome_assembly_tools
List of genome assembly tools
Inspector
A tool for evaluating long-read de novo assembly results
Mauve
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
metaRUpore
scripts to get reference.fasta and target list for metagenomic adaptive nanopore sequencing of complicated environmental microbiome
nf-testdata
Test datasets for nextflow pipelines.
nf_wochenende
A nextflow version of the Wochenende reference metagenome binning and visualization pipeline
pomoxis
Analysis components from Oxford Nanopore Research
Red
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
rustyread
A long read simulator based on badread idea