Nick Minor's Projects
A simple Nextflow wrapper that tells Freyja to do all the things
Anachronistic Lineage and Persistent INfection Explorer
Implementation of ALPINE components in Rust
Python BBDuk Wrapper for Filtering Paired Reads to Complete, 2-primer Amplicons
Sorts amplicons from Nanopore sequencing data based on similarity
PCR Amplicon-driven Haplotype Phasing
Python and Rust module for reporting results from the Amplityper viral amplicon phasing pipeline.
Quality control tool for identifying consensus sequences that over-index with reference sequence k-mers or primer sequences (WIP!)
Embarrassingly parallel checksums on large batches of files in pure Julia
Extremely fast checksum runner for arbitrarily large batches of files (WIP)
Stress-testing genomic cline models with spatially explicit downsampling
Benchmarking fastq compression with generic (mature) compression algorithms
Python module for deduplicating assembly contigs (or any sequence) in a FASTA and recalibrating any available depths
(WIP) Fast intermediate data representations for biological data. Don't put it in the minus-80—just put it on dry ice!
Halfmann and Minor et al. 2022 visualizations of a persistent SARS-CoV-2 infection that led to globally unique E484T mutation
Exploring signatures of maladaptation in areas of population decline
Shiny map of personal eBird targets
Convert a Genbank file with many extraneous Geneious annotations to EMBL format (even with of strict requirements as IPD)
Bespoke Python module for filtering a multi-sample VCF to a subset of individuals and then doing the same for CADD Scores
Bespoke Python script for slotting information into an Genbank file (for submission to IPD or wherever else)
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.
A simple Go module that rapidly and concurrently downloads an arbitrarily long list of files.
Go program for concurrently downloading a large number of allele sequences from the Immuno-Polymorphism Database
Metagenomic read classification well done.
Workflow for generating useful immunological gene allele databases
An overkill pipeline for sequencing read quality control and processing to test out some very cool bleeding edge tools
Wrap any command with lmk to get notification banners emails, or texts on exit code 0 (WIP)
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!)
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.
Multiple Allelic Comparison to Identify Candidate genes