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Doko-Miles Thorburn's Projects

agam_methylation icon agam_methylation

A pipeline designed for the Crisanti Lab for genome-wide methylation calls using ONT Fast5 data

balancing_selection_scan icon balancing_selection_scan

A genome-wide scan for balancing selection using various metrics, including Tajima's D, Wattersons Estimator, NCD, LD, Ne, and neutral simulations

genomic_read_processing icon genomic_read_processing

A nextflow pipeline developed to trim and map genomic reads to the Anopheles gambiae reference genome. This pipeline was originally developed for the Crisanti Lab.

ncd_genome_scan icon ncd_genome_scan

Modified scripts to generate NCD input files from VCFs, and calculate the NCD1 statistic.

origin_matters icon origin_matters

This repository is paired with a currently unpublished chapter on my PhD thesis and serves as a set of example scripts and pipelines used in the study. We investigated the impact of using a local reference genome on multiple commonly used metrics in population genomics. Additionally, we released a reference genome based on a European derived 2nd generation gynogen fish.

orthoexpress icon orthoexpress

Anopheles gambiae Orthology, Expression, & Gene Function Tool. Designed to aid in candidate gene searches.

protamine_exploration icon protamine_exploration

A project in the Cristanti Lab exploring the protamine genes. Also contains the nextflow phylogenetic tree construction pipeline.

rb_automation icon rb_automation

A collection of tools and protocols to increase throughput of existing methods used in the dry and wet lab.

rnaseq_workflows icon rnaseq_workflows

A nextflow pipeline that conducts the STAR 2-pass mapping steps for variant calling RNA-seq data with GATK (See Genomic_Read_Processing repo).

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