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nextstrain /ncov

Nextstrain build for SARS-CoV-2

pathogen nextstrain ncov sars-cov-2

UpdatedOct 24, 2025
Python

sanger-pathogens /Roary

Rapid large-scale prokaryote pan genome analysis

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedNov 3, 2025
Perl

ncbi /amr

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

bioinformatics genomics pathogen antibiotic-resistance

UpdatedSep 26, 2025
C++

sanger-pathogens /snp-sites

Finds SNP sites from a multi-FASTA alignment file

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedDec 16, 2020
C

sanger-pathogens /Artemis

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

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedJun 15, 2024
Java

sanger-pathogens /circlator

A tool to circularize genome assemblies

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedApr 6, 2024
Python

nickjcroucher /gubbins

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

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedAug 27, 2025
Python

sanger-pathogens /ariba

Antimicrobial Resistance Identification By Assembly

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedOct 12, 2023
Python

nf-core /taxprofiler

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

workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling microbiome illumina long-reads taxonomic-classification nf-core taxonomic-profiling

UpdatedNov 5, 2025
Nextflow

pathongs

indexofire /pathongs

Pathogen NGS Documentary

bioinformatics pathogen ngs genomic-epidemiology hzcdc

UpdatedApr 18, 2024

sanger-pathogens /assembly-stats

Get assembly statistics from FASTA and FASTQ files

bioinformatics research genomics pathogen sequencing next-generation-sequencing global-health infectious-diseases

UpdatedMay 9, 2023
C++

AncientMetagenomeDir

SPAAM-community /AncientMetagenomeDir

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

metadata pathogen metagenomics dataset microbiome archaeology ancient-dna metagenomics-data palaeogenomics sedadna

UpdatedOct 30, 2025
HTML

sanger-pathogens /pathogen-informatics-training

bioinformatics research genomics pathogen sequencing next-generation-sequencing global-health infectious-diseases

UpdatedJan 6, 2021
Jupyter Notebook

sanger-pathogens /Fastaq

Python3 scripts to manipulate FASTA and FASTQ files

bioinformatics research genomics pathogen sequencing next-generation-sequencing global-health infectious-diseases

UpdatedMar 24, 2025
Python

sanger-pathogens /iva

de novo virus assembler of Illumina paired reads

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedMay 17, 2021
Python

sanger-pathogens /assembly_improvement

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

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedJan 4, 2021
Perl

nextstrain /seasonal-flu

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

pathogen nextstrain

UpdatedNov 4, 2025
Python

nextstrain /mpox

Nextstrain build for mpox virus

metadata bioinformatics pipeline pathogen phylogenetics genbank augur nextstrain auspice virus-evolution genomic-epidemiology monkeypox mpox

UpdatedNov 5, 2025
Python

andrewjpage /tiptoft

Predict plasmids from uncorrected long read data

bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

UpdatedOct 31, 2025
Python

nextstrain /ncov-ingest

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.

python bash pathogen genbank nextstrain ncov sars-cov-2 gisaid

UpdatedOct 31, 2025
Python

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