Johannes Debler's repositories
orthofinder_extractor
Extract species specific orthogroups from Orthofinder results
docker_bonito
bonito basecaller docker image with cuda
docker_megalodon_guppy
Megalodon and Guppy GPU
nanopore_kit14_assembly
fungal genome assembly from Q20+ nanopore reads
bioinformatics
bifo scripts
docker_guppy
A dockerfile to build the latest version of GPU guppy basecaller
nextflow-annotate
Workflows I find helpful for fungal genome annotation
nf-assembly
Assembly and basic annotation of Illumina short reads
2018-10-15-annotations
Annotation scripts for several ascochyta isolates
Augustus
Genome annotation with AUGUSTUS
biocode
Bioinformatics code libraries and scripts
contiGC
determine per contig / scaffold GC content
docker-REPET
The REPET package in a container.
EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
effector_selection
Python script that scrapes the output of deepsig, effectorP, Interproscan (including SignalP) and selects effector candidates
fasta2audio
make fasta files audible
FixFAST5
Fixing Oxford Nanopore FAST5 files which are missing entries
interproscan_parse
Python3 script to parse interproscan output for keywords and create a fasta file with hits
judge_timer
A little Arduino timer for judging indoor skydiving
nanopore_LSK109_assembly
Assembly pipeline for Nanopore LSK109 chemistry on R9 flowcells
nf-occultercut
compare and plot GC content of genomes
nf-repeatmasking
Nextflow workflow for automatic repeat detection, classification and masking
nf-repeats
annotate repeats
pante2
🍄 🧬An (improved) pipeline for predicting and masking transposable elements in multiple fungal genomes.
predector
Effector prediction pipeline based on protein properties.
SporeCounter
Android App that lets you count spores (or other cells) under the microscope and then calculates amount per mL.