Stars
The second version of the Kraken taxonomic sequence classification system
💾 📃 "Reads to report" for public health and clinical microbiology
Nextflow pipeline for Neisseria gonorrhoeae isolate genome analysis
🔥🌿🐦🔥PhyloPHoeNIx: Pipeline for relatedness determination using PHoeNIx output.
Pipeline to generate NGS reads from a phylogeny
a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
A pipeline for running AMRfinderPlus and collating results into functional classes
Ultra-deep search for novel viruses
A simple pipeline for bacterial assembly and quality control
Materials for the STAMPS 2024 course at the MBL in Woods Hole, MA, USA
This repository contains tools and resources developed by Team Prasad Feldgarden during the "Resistance is Futile: A Codeathon to Combat Antimicrobial Resistance" (September 2024), hosted by NCBI a…
The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne …
Bacterial Identification and Antimicrobial Resistance
Nanopore assembly workflow from basecalled reads to polished assembly plus assembly QC, metrics, and plasmid replicon detection
This repository hosts a large collection of Nextflow snippets
A Nextflow pipeline to analyze NGS data in fastq format from bacterial genome
Finding regions of similarity between plasmids
🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens
A simple script to calculate q20/q30 percentages of a fastq file (can be gzipped)
A curated collection of Nextflow implementation patterns
Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories