Pinned Repositories
coiaf
Complexity of Infection Estimation with Allele Frequencies
coiaf-real-data
MalariaGEN Plasmodium falciparum Community Project analysis using coiaf
docker-SeekDeep
A dockerfile for building a docker with all needed libraries for SeekDeep
map_fastqs_snakemake
a snakemake pipeline for mapping fastq entries to a bowtie2 indexed reference genome
miplicorn
A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
MIPTools
A suite of computational tools used for molecular inversion probe design, data processing, and analysis.
MIPWrangler
Bioinformatics tools to analyze molecular inversion probe (MIP) sequencing results
SeekDeep
Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab
seekdeep_analysis_snakemake
Analyzes seekdeep data for read counts of individual samples
seekdeep_illumina_snakemake
a basic workflow for running seekdeep pipelines in snakemake
Bailey Lab's Repositories
bailey-lab/SeekDeep
Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab
bailey-lab/MIPTools
A suite of computational tools used for molecular inversion probe design, data processing, and analysis.
bailey-lab/miplicorn
A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
bailey-lab/map_fastqs_snakemake
a snakemake pipeline for mapping fastq entries to a bowtie2 indexed reference genome
bailey-lab/MIPWrangler
Bioinformatics tools to analyze molecular inversion probe (MIP) sequencing results
bailey-lab/seekdeep_analysis_snakemake
Analyzes seekdeep data for read counts of individual samples
bailey-lab/seekdeep_illumina_snakemake
a basic workflow for running seekdeep pipelines in snakemake
bailey-lab/seekdeep_nanopore_snakemake
a basic workflow for running seekdeep on nanopore
bailey-lab/BL-Survival-Prediction-and-Prognostic-Subgrouping
bailey-lab/coatswga
bailey-lab/EBV-SWGA
bailey-lab/merge_probe_sets
merges probe sets of several project resources to create a new project_resources directory
bailey-lab/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.
bailey-lab/wrangler_by_sample
runs individual samples through miptools wrangler as independent job submissions before final population-wide analysis
bailey-lab/automated_demultiplexing
automates the process of demultiplexing illumina runs
bailey-lab/coiaf-manuscript-work
Code and figures for the coiaf publication
bailey-lab/compilerProfiler
C++ library with an aligner to test different compiler speeds with different optimizations
bailey-lab/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.
bailey-lab/map_mip_arms
maps the arms of a mip panel to a genome
bailey-lab/map_nonref_SNPs
bailey-lab/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.
bailey-lab/miplithon
for messing around with python/snakemake implementations of miplicorn types of functions
bailey-lab/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
bailey-lab/MSMT_2021_DR_analyses
bailey-lab/pfsmarrt_cameroon_7-6-24
these are scripts used to analyze pfsmarrt amplicon performance on control datasets and 100 samples from dschang_cameroon
bailey-lab/Po_popgen_snakemake
bailey-lab/Repo_Template
A template for organizing and performing analysis (adapted from https://github.com/PhanstielLab/project-template).
bailey-lab/seekdeep_vs_bwa
snakemake pipeline for comparing observed extracted seekdeep reads against expected reads as judged by bwa
bailey-lab/selmar
Analysis of selection coefficients for antimalarial resistance
bailey-lab/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