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Thomas Hackl (thackl)

thackl

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Company:University of Groningen

Location:Groningen, Netherlands

Home Page:https://research.rug.nl/en/organisations/hackl-lab-eco-evolutionary-bioinformatics

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Thomas Hackl's starred repositories

thunderbird-android

K-9 Mail – Open Source Email App for Android

Language:KotlinLicense:Apache-2.0Stargazers:9841Issues:361Issues:4490

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Language:CLicense:GPL-3.0Stargazers:1499Issues:107Issues:300

tsv-utils

eBay's TSV Utilities: Command line tools for large, tabular data files. Filtering, statistics, sampling, joins and more.

Language:DLicense:BSL-1.0Stargazers:1418Issues:39Issues:46

emacs-async

Simple library for asynchronous processing in Emacs

Language:Emacs LispLicense:GPL-3.0Stargazers:831Issues:31Issues:126

Flye

De novo assembler for single molecule sequencing reads using repeat graphs

Language:CLicense:NOASSERTIONStargazers:739Issues:28Issues:672

OrthoFinder

Phylogenetic orthology inference for comparative genomics

Language:PythonLicense:GPL-3.0Stargazers:657Issues:27Issues:889

gggenomes

A grammar of graphics for comparative genomics

Language:RLicense:NOASSERTIONStargazers:577Issues:12Issues:152

wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Language:CLicense:GPL-3.0Stargazers:501Issues:31Issues:252

gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

Language:RStargazers:485Issues:6Issues:76

verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Language:PythonStargazers:275Issues:17Issues:257

VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data

Language:PythonLicense:GPL-2.0Stargazers:207Issues:4Issues:205

KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

Language:C++License:GPL-3.0Stargazers:200Issues:23Issues:162

ggplot2-exts.github.io

A list of ggplot2 extensions

Language:JavaScriptStargazers:159Issues:28Issues:28

AliTV

Visualize whole genome alignments as linear maps

Language:HTMLLicense:MITStargazers:67Issues:10Issues:108

proovread

PacBio hybrid error correction through iterative short read consensus

Language:PerlLicense:MITStargazers:60Issues:11Issues:138

Balrog

Bacterial Annotation by Learned Representation of Genes

Language:Jupyter NotebookLicense:MITStargazers:54Issues:8Issues:10

biozsh

the z in bioinformatics

Language:ShellLicense:MITStargazers:33Issues:4Issues:8

starfish

starfish: a modular toolkit for giant mobile element annotation

Language:PerlLicense:AGPL-3.0Stargazers:26Issues:3Issues:12

seq-scripts

scripts for sequence and feature conversion, annotation, analysis ...

Language:PerlLicense:MITStargazers:24Issues:3Issues:2

ont-assembly-snake

Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.

Language:PythonLicense:MITStargazers:17Issues:4Issues:16

pangenome_graphs

Constructing pan genome graphs from "protein family" assignments

Language:PythonStargazers:10Issues:6Issues:7

SeqFilter

Versatile FASTA/FASTQ sequence file analysis and modification tool

Language:PerlLicense:MITStargazers:9Issues:7Issues:10

detectEVE

Find endogenous viral elements in genomes

Language:PythonLicense:MITStargazers:9Issues:2Issues:19

cross-species-scaffolding

Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references

Language:ShellLicense:MITStargazers:8Issues:2Issues:5

two_marker_metabarcoding

Pipeline for metabarcoding of fungi with more than one marker (5.8S and ITS2)

Language:PythonLicense:LGPL-3.0Stargazers:6Issues:0Issues:0

long_read_metabarcoding

Pipeline for analysis of long DNA reads (in this case PacBio) for fungi metabarcoding using SSU, ITS and LSU as marker region

Language:PythonLicense:GPL-3.0Stargazers:5Issues:0Issues:0

pro-tycheposons

Supplementary code and data for mobile genetic elements in Prochlorococcus

Language:RLicense:NOASSERTIONStargazers:5Issues:3Issues:5

GVDB

Giant Virus Database

Stargazers:3Issues:0Issues:0

Longhurst-Province-Finder

Determines Longhurst Province for a given Lat/Long coordinate

Language:PythonStargazers:1Issues:2Issues:0