Bailey Lab

SeekDeep

Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab

MIPTools

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

miplicorn

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

map_fastqs_snakemake

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

MIPWrangler

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

seekdeep_analysis_snakemake

Analyzes seekdeep data for read counts of individual samples

seekdeep_illumina_snakemake

a basic workflow for running seekdeep pipelines in snakemake

seekdeep_nanopore_snakemake

a basic workflow for running seekdeep on nanopore

BL-Survival-Prediction-and-Prognostic-Subgrouping

coatswga

EBV-SWGA

nano_mamp_pipes

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.

automated_demultiplexing

automates the process of demultiplexing illumina runs

coiaf-manuscript-work

Code and figures for the coiaf publication

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.

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.

miplithon

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

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

MSMT_2021_DR_analyses

pfsmarrt_cameroon_7-6-24

these are scripts used to analyze pfsmarrt amplicon performance on control datasets and 100 samples from dschang_cameroon

Po_popgen_snakemake

Repo_Template

A template for organizing and performing analysis (adapted from https://github.com/PhanstielLab/project-template).

seekdeep_vs_bwa

snakemake pipeline for comparing observed extracted seekdeep reads against expected reads as judged by bwa

selmar

Analysis of selection coefficients for antimalarial resistance

wrangler_by_sample

runs individual samples through miptools wrangler as independent job submissions before final population-wide analysis

wrangler_snakemake

this is a re-implementation of the miptools wrangler singularity app, but with Nick's component C++ programs split out into separate rules for benchmarking