The Zavolab Automated RNA-seq Pipeline

A DSL for data-driven computational pipelines

R Interface to the jQuery Plug-in DataTables

software to identify primers that can distinguish genomes

Follow up to Grace Blackwell's 661k dataset, for 2023

Guide on shell scripting with Shellman vscode snippet

vscode shell script snippet extension

ATLAS - Three commands to start analyzing your metagenome data

interactive plots for differential expression analysis

Evaluating Nanopore-based bacterial variant calling

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

singularity & snakemake workflow to annotate genomes.

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several close…

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Gff-toolbox is a toolbox of commands that enables one to get the gist of their GFF annotation files, as well as to analyse them in different ways.

easy_circos is a simple conda package that aims on rapidly and easily creating minimal circos configurations templates based on input data.

Synteny and Rearrangement Identifier

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

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

De-Novo Repeat Discovery Tool

Extensive de-novo TE Annotator

Sphinx documentation source for a computational genomics tutorial.

Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs

a tool to filter sites in a FASTA-format whole-genome pseudo-alignment

Tool for plotting sequencing data along genomic coordinates.

allows user-friendly creation of user-defined pathways and mapping of experimental data on them

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.

Pout2Prot converts Percolator output files to protein group and subgroup files using Occam's razor or anti-Occam's razor. These output files can directly be used in Prophane for further downstream …

Assembled Genomes Compressor