pathogen

Nextstrain build for SARS-CoV-2

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Rapid large-scale prokaryote pan genome analysis

Finds SNP sites from a multi-FASTA alignment file

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

A tool to circularize genome assemblies

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

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Antimicrobial Resistance Identification By Assembly

Pathogen NGS Documentary

Get assembly statistics from FASTA and FASTQ files

Repository containing lists of all published ancient metagenomic (and related) samples and libraries

Python3 scripts to manipulate FASTA and FASTQ files

Scripts. config, and snakefiles for seasonal-flu nextstrain builds

de novo virus assembler of Illumina paired reads

Improve the quality of a denovo assembly by scaffolding and gap filling

Nextstrain build for mpox virus

Predict plasmids from uncorrected long read data

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.