Niklas Schandry's repositories
nf-genomeassembly
Nextflow pipeline to assemble genomes from long reads.
Knoch_et_al_transcriptomes
Scripts and files for the transcriptome analysis for Knoch et al., 2022
nf-annotate
(Plant) genome annotation pipeline
syri_gggenomes
Plot SyRi output via gggenomes
16S_Metagenomics_Coursefiles
A public version of the teaching repository, scrubbed to not include the actual data.
aradeepopsis-1
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
configs
Config files used to define parameters specific to compute environments at different Institutions
gggenomes
A grammar of graphics for comparative genomics
HRP
The full-length Homology-based R-gene Prediction (HRP) pipeline to comprehensively identify full-length NB-LRR gene models within genome assemblies.
models
Models and examples built with TensorFlow
nanoseq
Nanopore demultiplexing, QC and alignment pipeline
nextflow
A DSL for data-driven computational pipelines
nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
PCA_Visual
This repository contains a visual approach to Principal Component Analysis of more than three vectors
SLR
Scaffolding using long reads obtained by the third generation sequencing technologies.
test-datasets
Test data to be used for automated testing with the nf-core pipelines