CDCgov / phoenixLinks
π₯π¦π₯PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens
β86Updated this week
Alternatives and similar repositories for phoenix
Users that are interested in phoenix are comparing it to the libraries listed below
Sorting:
- Bioinformatics Pipeline and Visualization resourcesβ58Updated last year
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, esβ¦β41Updated last year
- PopPUNK π¨βπ€ (POPulation Partitioning Using Nucleotide Kmers)β100Updated 2 months ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic dataβ66Updated 3 years ago
- β71Updated this week
- Fast k-mer based tool for multi locus sequence typing (MLST)β45Updated 5 years ago
- Scripts and libraries for Environmental Genomicsβ38Updated 8 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)β62Updated 2 years ago
- Simple bacterial assembly and annotation pipelineβ78Updated last month
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.β32Updated 4 months ago
- Split Kmer Analysisβ65Updated 3 years ago
- Surveillance of pathogens using population genomics and sequencingβ43Updated 3 months ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequencesβ60Updated 3 weeks ago
- β54Updated 5 months ago
- Gene-flank analysis toolβ30Updated 9 months ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.β58Updated 6 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological dataβ41Updated last week
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWooβ¦β55Updated 3 years ago
- CRyPTIC data processing pipelinesβ34Updated last year
- β84Updated 2 years ago
- BEAV: Bacterial Element Annotation reVampedβ69Updated last month
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomiβ¦β67Updated 7 months ago
- π»βπ¨ Calculate distance matrix from ChewBBACA cgMLST allele call tablesβ29Updated 2 years ago
- Split k-mer analysis β version 2β92Updated 2 months ago
- A nextflow pipeline for decontamination of short reads, long reads and contigsβ54Updated 3 months ago
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermberβ65Updated last year
- hecatomb is a virome analysis pipeline for analysis of Illumina sequence dataβ59Updated 3 weeks ago
- A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.β49Updated 3 years ago
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remoβ¦β21Updated last week
- A scalable bacterial genome assembly, annotation and analysis pipelineβ74Updated last year