Nextstrain build for novel coronavirus SARS-CoV-2

A tool to circularize genome assemblies

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

Antimicrobial Resistance Identification By Assembly

Python3 scripts to manipulate FASTA and FASTQ files

de novo virus assembler of Illumina paired reads

Nextstrain build for mpox virus

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

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.

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Assembling the cause of phenotypes and genotypes from NGS data

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Nextstrain build for avian influenza viruses

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

Mycobacterial pipeline

Nextstrain build for dengue virus

Nextstrain build for Zika virus

SARS-CoV-2 variant growth rates and frequency forecasts

CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.