colindaven
Bioinformatician at KWS SAAT SE. Previously PhD and Postdoc/Staff scientist positions at Hannover Medical School. Nextflow, bioinformatics, metagenomics
Germany
Pinned Repositories
awesome-pangenomes
A list of software for pangenomics
blacklister
Improve your metagenomic reference sequence: Simple adapter and contamination FASTA masking using bowtie2 and bedtools
genometa
The shotgun metagenome analyzer genometa.
guppy_on_slurm
Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
jbrowse2_utils
Bash scripts for writing assemblies and tracks to JBrowse2 https://jbrowse.org/jb2/
rs_demultiplex
Simple demultiplexing of FASTQ, one oligo (barcode) at a time
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
nf_wochenende
A nextflow version of the Wochenende reference metagenome binning and visualization pipeline
Wochenende
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
colindaven's Repositories
colindaven/awesome-pangenomes
A list of software for pangenomics
colindaven/guppy_on_slurm
Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
colindaven/rs_demultiplex
Simple demultiplexing of FASTQ, one oligo (barcode) at a time
colindaven/jbrowse2_utils
Bash scripts for writing assemblies and tracks to JBrowse2 https://jbrowse.org/jb2/
colindaven/blacklister
Improve your metagenomic reference sequence: Simple adapter and contamination FASTA masking using bowtie2 and bedtools
colindaven/rusty_samplesheet
Very simple Illumina SampleSheet validation in Rust. Make your biologists check their own custom SampleSheets! Can be compiled for Windows users.
colindaven/wochenende_manuscript
Code accompanying the Wochenende metagenomics analyzer manuscript
colindaven/pafgnostic
colindaven/awesome-HiC
Awesome list of HiC data analysing tools
colindaven/awesome-nanopore
A curated list of awesome nanopore analysis tools.
colindaven/awesome-nextflow
A curated list of nextflow based pipelines
colindaven/DGE
Nextflow pipeline that runs DESeq2 on data processed with the nextflow RNAseq pipeline
colindaven/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
colindaven/docker-genomic-analysis
Basic docker image for ad-hoc genomic analyses
colindaven/genome_assembly_tools
List of genome assembly tools
colindaven/GINGER
colindaven/H-PoPG
H-PoP and H-PoPG: Heuristic Partitioning Algorithms for Single Individual Haplotyping of Polyploids
colindaven/Inspector
A tool for evaluating long-read de novo assembly results
colindaven/Liftoff
An accurate GFF3/GTF lift over pipeline
colindaven/Mauve
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
colindaven/metaRUpore
scripts to get reference.fasta and target list for metagenomic adaptive nanopore sequencing of complicated environmental microbiome
colindaven/modbam2bed
colindaven/nf-testdata
Test datasets for nextflow pipelines.
colindaven/nf_wochenende
A nextflow version of the Wochenende reference metagenome binning and visualization pipeline
colindaven/pomoxis
Analysis components from Oxford Nanopore Research
colindaven/raspir
Raspir, the rare species identifier
colindaven/Red
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
colindaven/rust-bio
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
colindaven/rustyread
A long read simulator based on badread idea
colindaven/smashpp
Find and visualize rearrangements in DNA sequences