Multi-user server for Jupyter notebooks

This is the development home of the workflow management system Snakemake. For general information, see

A python module for scientific analysis of 3D data based on VTK and Numpy

Fast genome-wide functional annotation through orthology assignment

Spatial Single Cell Analysis in Python

COBRApy is a package for constraint-based modeling of metabolic networks.

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Download FASTQ files from SRA or ENA repositories.

Deep functional residue identification

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Filtering and trimming of long read sequencing data

CarveMe: genome-scale metabolic model reconstruction

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

SemiBin: metagenomics binning with self-supervised deep learning

FUNGuild: parsing OTUs into functional guilds

FunGAP: fungal Genome Annotation Pipeline

MGnify genome analysis pipeline

Graph-based assembly phasing

Toolbox for comparative genomics of MAGs

All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

TidyMS: Tools for working with MS data in untargeted metabolomics

Splitting of sequence reads by internal adapter sequence search

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

Tool to estimate genome quality of microbial eukaryotes

KEGG Module Evaluation Tool

Automatic eukaryotic taxonomic classification

Biological sequence clustering tool with dynamic threshold

A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses