NCEZID-EDLB
Bioinformatics projects spanning the Bioinformatics Research and Development (BiRD) and Culture Independent and Metagenomics Subtyping (CIMS) Teams in EDLB
Pinned Repositories
AlleleCodes
Python script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies
BIOME-scripts
random scripts
datasets
Benchmark and toy datasets
HMAS-QC-Pipeline
A pipeline for performing quality control on HMAS data, in preparation for downstream MLST-like or AMR-like analyses.
HMAS-QC-Pipeline2
An analysis pipeline for initial quality control and denoising of highly-multiplexed amplicon sequencing (HMAS) data, now without using mothur (as was used in the previous version)
md5_reducer
Makes MD5sums with fewer bits using the Rust language
pn2.0-mlst-databases
Databases for wg/cgMLST analysis with the PN2.0 software
source-attribution-MLST
T3Pio
trapical
trapical: trapical rapidly aligns Pulsenet islolate core alleles
NCEZID-EDLB's Repositories
ncezid-biome/pn2.0-mlst-databases
Databases for wg/cgMLST analysis with the PN2.0 software
ncezid-biome/HMAS-QC-Pipeline2
An analysis pipeline for initial quality control and denoising of highly-multiplexed amplicon sequencing (HMAS) data, now without using mothur (as was used in the previous version)
ncezid-biome/datasets
Benchmark and toy datasets
ncezid-biome/trapical
trapical: trapical rapidly aligns Pulsenet islolate core alleles
ncezid-biome/AlleleCodes
Python script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies
ncezid-biome/HMAS-QC-Pipeline
A pipeline for performing quality control on HMAS data, in preparation for downstream MLST-like or AMR-like analyses.
ncezid-biome/BIOME-scripts
random scripts
ncezid-biome/hash_sequence
A Rosetta Stone for getting hashsums
ncezid-biome/md5_reducer
Makes MD5sums with fewer bits using the Rust language
ncezid-biome/MIDAS2
Metagenomic Intra-Species Diversity Analysis 2
ncezid-biome/source-attribution-MLST
ncezid-biome/T3Pio
ncezid-biome/ANI-paper
ncezid-biome/EDLB-micropipe-LATEST
Latest Production Version of EDLB's version of Micropipe
ncezid-biome/HMAS-Internal-Validation
This repository contains scripts and other documents pertaining to internal validation of the HMAS QC pipeline.
ncezid-biome/INNUENDO_docker
Docker-compose for INNUENDO Platform deployment
ncezid-biome/INNUENDO_REST_API
Frontend application and REST API for the INNUENDO Platform
ncezid-biome/INNUENDO_schemas
repository for the INNUENDO chewbbaca schemas
ncezid-biome/nanoporeWorkflow
Nextflow workflows created to address a variety of CDC-EDLB Nanopore sequencing bioinformatics needs
ncezid-biome/ncbi-one-liners
A collection of NCBI one-liners
ncezid-biome/NGSU_LibPrep_2021
ncezid-biome/tripod
An analysis pipeline for checking the performance of stool_HMAS, isolate_HMAS, isolate_WGS data sets
ncezid-biome/espwAlleleCaller
Software to automatically call the espW allele in STEC genomes
ncezid-biome/ncezid-biome.github.io
ncezid-biome/prodigal_training_files
species specific training files based on specific reference genomes