CDCgov / phoenix
π₯π¦π₯PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
β52Updated this week
Related projects: β
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositoriesβ32Updated last week
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenomeβ46Updated last year
- Bioinformatics Pipeline and Visualization resourcesβ53Updated 3 weeks ago
- β19Updated this week
- π»βπ¨ Calculate distance matrix from ChewBBACA cgMLST allele call tablesβ25Updated 11 months ago
- Predict plasmids from uncorrected long read dataβ39Updated 4 years ago
- Working with the outputs of sourmash in Rβ22Updated 10 months ago
- BEAV: Bacterial Element Annotation reVampedβ55Updated 2 weeks ago
- Recombination-free treesβ55Updated last year
- β43Updated 2 months ago
- Split k-mer analysis β version 2β57Updated last month
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatβ¦β51Updated last month
- Miscellaneous Perl scripts from 20 years in microbial bioinformaticsβ16Updated 2 months ago
- whole genome MLST analysisβ35Updated 4 months ago
- Read Assembly and Annotation Pipeline Toolβ56Updated 4 months ago
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermberβ51Updated 2 weeks ago
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.β13Updated 3 weeks ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPsβ25Updated last month
- Collection of R scripts for SARS-CoV-2 (variant) analysesβ12Updated last year
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomiβ¦β31Updated last week
- Automatic Assembly For The Fungiβ19Updated last year
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.β27Updated 4 months ago
- Metagenomic Analysis in Real Timeβ17Updated last month
- Influenza genome analysis Nextflow workflowβ22Updated last month
- Ley Lab MetaGenome Profiler DataBase generatorβ45Updated last year
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.β14Updated 4 months ago
- Discover and annotate the viromeβ29Updated 5 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes databaseβ39Updated 3 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic dataβ56Updated 2 years ago
- Gene-flank analysis toolβ25Updated 4 months ago