Bailey Lab
bailey-lab
Studying the genetics and genomics of infectious disease and immunity
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Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab
A suite of computational tools used for molecular inversion probe design, data processing, and analysis.
A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
Complexity of Infection Estimation with Allele Frequencies
Coverage Optimizing and Accurate Toolkit for selective whole genome amplification (sWGA)
a snakemake pipeline for mapping fastq entries to a bowtie2 indexed reference genome
Repositories
50repo for a manuscript describing msmt longitudinal data from 2021-2023
A suite of computational tools used for molecular inversion probe design, data processing, and analysis.
Coverage Optimizing and Accurate Toolkit for selective whole genome amplification (sWGA)
A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
when demultiplexing fails, we need the ability to figure out which sample barcodes were present and in what abundances. This allows us to figure out if the 'wrong' barcodes were applied to the samples or if the barcoding failed.
C++ library with an aligner to test different compiler speeds with different optimizations
Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab
uses Nick Hathaway's variantCallOnSeqAndProtein script to call variants on vcf files and generate prevalences and amino acid calls
Complexity of Infection Estimation with Allele Frequencies
a snakemake pipeline for mapping fastq entries to a bowtie2 indexed reference genome
maps the arms of a mip panel to a genome
No description provided.
converts amino acid counts files into miptools formatted counts that are suitable for prevalence estimates
a basic workflow for running seekdeep pipelines in snakemake
a snakemake repo for mapping regional mutations in R
growing set of utility scrips supporting lab work in the bailey lab
these are scripts used to analyze pfsmarrt amplicon performance on control datasets and 100 samples from dschang_cameroon
No description provided.
merges probe sets of several project resources to create a new project_resources directory
No description provided.
Analyzes seekdeep data for read counts of individual samples
a basic workflow for running seekdeep on nanopore
A template for organizing and performing analysis (adapted from https://github.com/PhanstielLab/project-template).
Analysis of selection coefficients for antimalarial resistance
No description provided.
NanoMAMP Pipes is a free-to-use one-step automated pipeline designed for comprehensive analysis of molecular inversion probe and amplicon sequencing data from Nanopore platforms.
No description provided.
for messing around with python/snakemake implementations of miplicorn types of functions
automates the process of demultiplexing illumina runs
runs individual samples through miptools wrangler as independent job submissions before final population-wide analysis