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Colorado State Public Health Laboratory
- Denver, Colorado, USA
- https://cdphe.colorado.gov/lab
- in/sam-baird-287800194
Highlights
- Pro
Stars
Scripts to wrap Terra API calls for programmatic workflow execution, workspace management, and data export to other platforms. Part of the workflow is specific to my environment, but hopefully it a…
Build data reports in 100% Python (a fork of Datapane)
The ARTIC field bioinformatics pipeline
Repository for suggesting new lineages that should be added to the current scheme
a service to allow people to register primers to be monitored for intersecting variants and be notified if new variants arise
Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification
a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
Predict MLST directly from uncorrected long reads
Follow up to Grace Blackwell's 661k dataset, for 2023
Bayesian inference of ancestral dates on bacterial phylogenetic trees
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
simple program to rotate a circular sequence to start at a given position or string
Basic workflow for nanopore sequencing data
resources for bioinformatics education
Reads mapping against target sequences, checking mapping and consensus sequences production
A genome visualization python package for comparative genomics
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
Ultra-deep search for novel viruses
Fast k-mer based tool for multi locus sequence typing (MLST)
Workflows and scripts for the assembly and analysis of SARS-CoV-2 whole genome tiled amplicon sequencing.
📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.