thackl

gggenomes

A grammar of graphics for comparative genomics

proovframe

frame-shift correction for long-read (meta)genomics

seq-scripts

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

cross-species-scaffolding

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

host-phage-tRNA-att-finder

Link phages and potential host by finding shared attachment sites for prophage integration

pro-tycheposons

Supplementary code and data for mobile genetic elements in Prochlorococcus

thacklr

A Collection of R Functions and Snippets I Often Use

detectEVE

Find endogenous viral elements in genomes

thackl.github.io

Source code of my homepage & blog

AliView

Software for aligning viewing and editing dna/aminoacid sequences, intuitive, fast and lightweight. Download and website:

google-sync

Scripts for syncing local tsv files with google spreadsheets

lecture-variant-calling

Variant-Calling-Example

plot-scripts

Quick plots directly in the terminal window

proovframe-benchmark

Benchmark data sets used to assess proovframe - frame-shift correction for long-read (meta)genomics

simons-metagenome-data-descriptor-map-figure

cb-emales

Supplementary code and data for endogenous mavirus-like elements in Cafeteria burkhardae genomes

circlator

A tool to circularize genome assemblies

cr-genomes

Supplementary code and data for genomes of C.roenbergensis: E4-10P, BVI, Cflag and RCC970-E3

gallery

Gallery of ggplot2 extensions

hmm-scripts

mbc

long-read-metabarcoding for eukaryotes

mbc-prime

Find group-specific primer binding sites for amplicon metabarcoding

omx-assemble-ont

A workflow for polished assemblies from nanopore data

omx-suite

A command line interface to omx-* snakemake workflows

org-anize

Navigate projects based on .org files and prespecified folder structures

phylo-scripts

scripts for working with phylogenic and taxonomic data

reactivated-endogenous-virophages

Supplementary data for Koslova et al. "Endogenous virophages in the marine protist Cafeteria burkhardae are active and mitigate giant virus infection"

sam-scripts

scripts for SAM/BAM analysis, conversion, modification, ...

ubuntu-setup

Things to setup and install on fresh ubuntu

zsh-setup

customized zsh configs and setup scripts