Nick Minor's repositories
E484T-visualizations
Halfmann and Minor et al. 2022 visualizations of a persistent SARS-CoV-2 infection that led to globally unique E484T mutation
ampl-BBDuk
Python BBDuk Wrapper for Filtering Paired Reads to Complete, 2-primer Amplicons
amplicon_sorter
Sorts amplicons from Nanopore sequencing data based on similarity
amplityper-report
Python and Rust module for reporting results from the Amplityper viral amplicon phasing pipeline.
compression_benchmark
Benchmarking fastq compression with generic (mature) compression algorithms
dedup_and_recal
Python module for deduplicating assembly contigs (or any sequence) in a FASTA and recalibrating any available depths
eBird-malAdapt
Exploring signatures of maladaptation in areas of population decline
gbk_switcheroo
Bespoke Python script for slotting information into an Genbank file (for submission to IPD or wherever else)
goDownloadFiles
A simple Go module that rapidly and concurrently downloads an arbitrarily long list of files.
goDownloadIPD
Go program for concurrently downloading a large number of allele sequences from the Immuno-Polymorphism Database
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.
MHC-I-allele-discovery
Nextflow pipeline for discovering new MHC Class I alleles in Rhesus and Cynomolgus Macaques (in development; coming soon!)
MHC-II-allele-discovery
Nextflow pipeline for discovering new MHC Class II alleles in Rhesus and Cynomolgus Macaques
nf-templates
Simple NextFlow Templates for Developing your own Workflows
prolonged-infection-suppfig1
Pipeline for examining Intrahost Nucleotide Variants for Halfmann et al. 2022
prolonged-infection-suppfig2
Pipeline for visually comparing mutations in a persistent SARS-CoV-2 infection with the virus globally
pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
readmerger
Tool for rapidly merging Oxford Nanopore FASTQ files. Never use cat and find again!
resplice-primers
Find all possible combinations of spike-in primers in an amplicon scheme
Sample-VCF-by-LatLong
Python script for downsampling a multi-sample VCF by the samples' geographic locations
SC2-read-downloader
Workflow for downloading SARS-CoV-2 reads from the Sequence Read Archive, while handling a variety of sequencing instruments and primer sets
snipit
snipit: summarise amino acid variants relative to a reference sequence
still
Unit testing for spreadsheets
tidy-my-VCF
A simple R script leveraging vcfR to reformat a VCF with "tidy" data principles