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2018-10-15-annotations

Annotation scripts for several ascochyta isolates

augustus

Genome annotation with AUGUSTUS

biocode

Bioinformatics code libraries and scripts

bioinformatics

bifo scripts

contigc

determine per contig / scaffold GC content

docker-repet

The REPET package in a container.

docker_bonito

bonito basecaller docker image with cuda

docker_guppy

A dockerfile to build the latest version of GPU guppy basecaller

docker_megalodon_guppy

Megalodon and Guppy GPU

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

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_kit14_assembly

fungal genome assembly from Q20+ nanopore reads

nanopore_lsk109_assembly

Assembly pipeline for Nanopore LSK109 chemistry on R9 flowcells

nextflow-annotate

Workflows I find helpful for fungal genome annotation

nf-assembly

Assembly and basic annotation of Illumina short reads

nf-augustus_with_rnaseq

nf-busco

nf-genomecoverage

nf-occultercut

compare and plot GC content of genomes

nf-repeatmasking

Nextflow workflow for automatic repeat detection, classification and masking

nf-repeats

annotate repeats

orthofinder_extractor

Extract species specific orthogroups from Orthofinder results

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.