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Hi there 👋

I'm a biologist who develops research software with an emphasis on reproducibility, ease-of-use, and performance. Before my current position in David H. O'Connor's group at University of Wisconsin - Madison, I worked in bird population genomics and speciation at University of Wyoming and University of Minnesota—Twin Cities. I've also worked in collection and database management at the Field Museum of Natural History in Chicago and the Bell Museum of Natural History in Saint Paul, Minnesota.

My research interests include:

  • population genomics
  • speciation and population divergence
  • evolutionary ecology
  • immunogenomics
  • disease ecology
  • scientific reproducibility
  • data visualization
  • simulations (especially with SLiM!)

My entry to programming, like many biologists, was R, and I still regularly do stats and data visualization with R. Nowadays, I do most of my scientific computing in Python, and for special applications, I'm a huge fan of Rust. To design pipelines and containerize software, I also write a fair amount in Nextflow and Docker, and to create in silico evolutionary simulations, I use SLiM.

Collaboration is one the best parts of science. If you also develop research software or work on some of the same topics, I'd love to connect, bounce off ideas, and make the most of open-source software development together.

Nick Minor's Projects

allthefreyjas icon allthefreyjas

A simple Nextflow wrapper that tells Freyja to do all the things

alpine icon alpine

Anachronistic Lineage and Persistent INfection Explorer

ampl-bbduk icon ampl-bbduk

Python BBDuk Wrapper for Filtering Paired Reads to Complete, 2-primer Amplicons

amplityper-report icon amplityper-report

Python and Rust module for reporting results from the Amplityper viral amplicon phasing pipeline.

april icon april

Quality control tool for identifying consensus sequences that over-index with reference sequence k-mers or primer sequences (WIP!)

bhasher.jl icon bhasher.jl

Embarrassingly parallel checksums on large batches of files in pure Julia

checkle icon checkle

Extremely fast checksum runner for arbitrarily large batches of files (WIP)

cline-cutter icon cline-cutter

Stress-testing genomic cline models with spatially explicit downsampling

dedup_and_recal icon dedup_and_recal

Python module for deduplicating assembly contigs (or any sequence) in a FASTA and recalibrating any available depths

dryice icon dryice

(WIP) Fast intermediate data representations for biological data. Don't put it in the minus-80—just put it on dry ice!

e484t-visualizations icon e484t-visualizations

Halfmann and Minor et al. 2022 visualizations of a persistent SARS-CoV-2 infection that led to globally unique E484T mutation

ebird-maladapt icon ebird-maladapt

Exploring signatures of maladaptation in areas of population decline

embl-my-gbk icon embl-my-gbk

Convert a Genbank file with many extraneous Geneious annotations to EMBL format (even with of strict requirements as IPD)

filter_vcf_and_cadd_scores icon filter_vcf_and_cadd_scores

Bespoke Python module for filtering a multi-sample VCF to a subset of individuals and then doing the same for CADD Scores

gbk_switcheroo icon gbk_switcheroo

Bespoke Python script for slotting information into an Genbank file (for submission to IPD or wherever else)

give-a-sheet icon give-a-sheet

Auto-generate type-validated, error-free input samplesheets for the nf-core pipeline you want to run. Pipeline support is limited at this stage, but more pipelines will be added in the future.

godownloadfiles icon godownloadfiles

A simple Go module that rapidly and concurrently downloads an arbitrarily long list of files.

godownloadipd icon godownloadipd

Go program for concurrently downloading a large number of allele sequences from the Immuno-Polymorphism Database

krummholz icon krummholz

An overkill pipeline for sequencing read quality control and processing to test out some very cool bleeding edge tools

letmeknow icon letmeknow

Wrap any command with lmk to get notification banners emails, or texts on exit code 0 (WIP)

lgc icon lgc

Let's Get Coding! A command line tool that creates template files and configures a development environment for projects in a variety of languages (work in progress!)

lowcov-wgs icon lowcov-wgs

A NextFlow Pipeline inspired by Lou et al. 2021 (Molecular Ecology). Its purpose is to collate and streamline tools used to analyze WGS data with low sequencing effort per sample.

macic icon macic

Multiple Allelic Comparison to Identify Candidate genes

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