⚡ ♒ Rapid prokaryotic genome annotation

Prodigal Gene Prediction Software

adapter trimmer for Oxford Nanopore reads

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

Hierarchical clustering of cgMLST

MAnorm2 for Normalizing and Comparing ChIP-seq Samples

To pre-process a set of ChIP-seq samples and coordinate with MAnorm2 for differential analysis

dcHiC: Differential compartment analysis for Hi-C datasets

TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

De novo assembler for single molecule sequencing reads using repeat graphs

a tool for inferring species tree from sequencing reads

Human Influenza classification web app

Detect contigs of complete circular genomes

Ultra-fast and memory-efficient (meta-)genome assembler

INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Some collected tools for molecular simulation pipelines

OFFICIAL: AnteChamber PYthon Parser interfacE

AutoDock for GPUs and other accelerators

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

The MLST pipeline developed by the PathOGiST research group

BSR-Based Allele Calling Algorithm

🆔 Scan contig files against PubMLST typing schemes