Segmented HAPlotype Estimation and Imputation Tool

A tool for generating consensus long-read assemblies for bacterial genomes

Haplotype based scans for selection

Graph-based assembly phasing

MGnify genome analysis pipeline

Useful bash one-liners for bioinformatics.

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

Deep functional residue identification

DAS Tool

Robs manual for the computational genomics and bioinformatics class.

KEGG Module Evaluation Tool

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

Metabolomics Spectrum Resolver/Displayer

A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets

Download FASTQ files from SRA or ENA repositories.

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

A Python package for exploring and analysing genetic variation data

Using MASST or fastMASST, adding metadata onto a tree ontology for microbes

SemiBin: metagenomics binning with self-supervised deep learning

SortMeRNA: next-generation sequence filtering and alignment tool

Metabolic scanning and annotation of Metagenomes

HMMER: biological sequence analysis using profile HMMs

Assigning precursor-product ion relationships in indiscriminant MS/MS data

Analyzing and visualizing KEGG information using the grammar of graphics

Filter SAM file for soft and hard clipped alignments