KatharinaHoff

Katharina Hoff's starred repositories

cactus

Official home of genome aligner based upon notion of Cactus graphs

Language:CNOASSERTION498 21 822

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Language:PerlNOASSERTION343 21 776

Augustus

Genome annotation with AUGUSTUS

Language:C++277 18 276

GetOrganelle

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

Language:PythonGPL-3.0259 11 243

alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

MIT206 24 1

odp

oxford dot plots

Language:PythonGPL-3.0127 5 77

bluesky-crossposter

An app for crossposting your posts from bluesky to twitter and mastodon

Language:Python104 4 18

assembly-stats

Assembly statistic visualisation

Language:JavaScriptMIT88 5 19

BEND

Benchmarking DNA Language Models on Biologically Meaningful Tasks

Language:PythonBSD-3-Clause83 5 18

aviary

A hybrid assembly and MAG recovery pipeline (and more!)

Language:PythonGPL-3.076 5 114

LoReAn

Long Reads Annotation pipeline

Language:PythonMIT70 8 46

ProtHint

Protein hint generation pipeline for gene finding in eukaryotic genomes

Language:PythonNOASSERTION53 4 52

MakeHub

Fully automated generation of UCSC assembly hubs

Language:PythonGPL-3.033 4 8

This package provides a function to reformat lists of genome coverage files, such as bigWig of bam files, into the directory structure of a UCSC Track Hub ready to be visualized in the genome browser. For details about it's use, please have a look at the vignette of the package.

Language:HTMLGPL-3.027 50