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asua-jid-2020

This repository contains the data accompanying the paper titled "Changing Prevalence of Potential Mediators of Aminoquinoline, Antifolate, and Artemisinin Resistance Across Uganda"

automated_demultiplexing

automates the process of demultiplexing illumina runs

bl-survival-prediction-and-prognostic-subgrouping

coatswga

coiaf

Complexity of Infection Estimation with Allele Frequencies

coiaf-manuscript-work

Code and figures for the coiaf publication

coiaf-real-data

MalariaGEN Plasmodium falciparum Community Project analysis using coiaf

compilerprofiler

C++ library with an aligner to test different compiler speeds with different optimizations

count_undetermined_sample_barcodes

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.

cppprogutils

C++ program utils with classes to handle option parsing and with optional sub program

deploy-singularity-testing

Testing the use of Github Actions to deploy singularity images

docker-seekdeep

A dockerfile for building a docker with all needed libraries for SeekDeep

ebv-swga

ebv_cox-regression

EBV Cox Regression Bootstraps and Cross Validation Model For Risk Assessment of EBV and Other Features.

ephi-hrp-2021

hrp3

labman_scripts

growing set of utility scrips supporting lab work in the bailey lab

lastz

Program for aligning DNA sequences, a pairwise aligner.

map_fastqs_snakemake

a snakemake pipeline for mapping fastq entries to a bowtie2 indexed reference genome

map_mip_arms

maps the arms of a mip panel to a genome

map_nonref_snps

merge_probe_sets

merges probe sets of several project resources to create a new project_resources directory

merge_samplesheets

this is a wrapper for Jeff's program that merges samplesheets. Written to allow an easy record of settings used to produce each merged sample sheet.

miplicorn

A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.

miplithon

for messing around with python/snakemake implementations of miplicorn types of functions

mipscripts

Various tools for use wth MIPTools pipelines

miptools

A suite of computational tools used for molecular inversion probe design, data processing, and analysis.

miptools_analysis_no_jupyter

This is a snakemake pipeline to run miptools analysis without jupyter. It's based off of Ozkan's analysis_template_with_qual.ipynb

mipwrangler

Bioinformatics tools to analyze molecular inversion probe (MIP) sequencing results

msmt_2021_dr_analyses