a python command-line tool which draws basic graphs in the terminal

Scripts to download genomes from the NCBI FTP servers

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

Fast genome-wide functional annotation through orthology assignment

Use a text editor. Make a PDF.

Gene cluster comparison figure generator

ATLAS - Three commands to start analyzing your metagenome data

Read-based phasing of genomic variants, also called haplotype assembly

python Circos

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

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

A genome visualization python package for comparative genomics

Download FASTQ files from SRA or ENA repositories.

Tool for plotting sequencing data along genomic coordinates.

Build a partitioned pangenome graph from microbial genomes

This Snakemake pipeline implements the GATK best-practices workflow

Generating Covid-19 Analytics Report PDFS with Python

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

The uncompromising Snakemake code formatter

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

A console-based alignment viewer

Antibiotic resistance prediction in minutes

Reorients assembled microbial sequences

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)