Stars
Mac app that shows all open files, directories, sockets, pipes and devices in use by all running processes. Nice GUI for lsof.
Multi-user server for Jupyter notebooks
This is the development home of the workflow management system Snakemake. For general information, see
Making Protein folding accessible to all!
A python module for scientific analysis of 3D data based on VTK and Numpy
MMseqs2: ultra fast and sensitive search and clustering suite
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
De novo assembler for single molecule sequencing reads using repeat graphs
The second version of the Kraken taxonomic sequence classification system
💡 Easily improve the user experience of your Shiny apps in seconds
A single molecule sequence assembler for genomes large and small.
Fast genome-wide functional annotation through orthology assignment
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
COBRApy is a package for constraint-based modeling of metabolic networks.
JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
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
HMMER: biological sequence analysis using profile HMMs
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files