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mashtree
🌳 Create a tree using Mash distancesfasten
👷 Fasten toolkit, for streaming operations on fastq filesawesome-bioinformatics-education
resources for bioinformatics educationKalamari
🐙 A curated database of completed assemblies with taxonomy IDsawesome-bioinformatics-jobs
Resources for bioinformatics jobslyve-SET
💃 🌴 LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigationslskScripts
A placeholder for all my random scripts. Some scripts might eventually graduate and go to their own projects, so don't be surprised if anything leaves in the future.pdtk
NCBI Pathogen Detection Portal toolkitCG-Pipeline
Genome assembly/prediction/annotation pipeline for the Linux command lineannapotater
Quick and dirty SNP annotatormlst-hash-template
This is a template for any new hash-based MLST databaseis-it-down
BookAI
Machine learning for making my noveltaxdb
Manipulate taxonomy databaseslskatz.github.io
Website for Lee Katzlyve-KSNP
a set of wrapper scripts for KSNPhashest
estimate MLST with hashescgMLST-comparison
naughty-binfie-files
container-test
Test building containersfile-find-fast
File::Find::Fastadvent-of-code
https://adventofcode.com/hash2seq
Given a reference sequence and a hash, reverse engineer what the sequence isMLST-CLI
Make a database of wgMLST alleles and manipulate itreadTaxonomy
Methods in various languages for how to create a fast database from NCBI Taxonomyperl-app-hump
🐫 A perl module for workflow dependencies.nextflow-perl
a very superficial attempt to replace nextflow's java engine with perlSARS-CoV-2-trueTree
True tree for a SARS-CoV-2 phylogenyROSS
ROSS - Random Operations on Sequences Suiteperl-mash
perl module for Mash sketchestemplate-perl
A simple template for perl projectstest-github-cache
Testing github actions cachingBio--Kmer
A perl module for kmer countingSuffix--trie
Pure Perl suffix triesha256emoji
Create an emoji hashsum from a filebiophp-at-ga-tech
Bioinformatics tools for PHPSchedule--SGELK
Perl module for scheduling tasks, with only using qsub/qstat/qdel. A very portable scheduler.callsam
Call variants on sam filesany2index
biophp
Lee Katz's BioPHPtaco-bell-locations
Print zip codes of taco bell locations.what3wordsRegion
Give a list of "what 3 words" for a regionncbiClusters
Lyve-SET-paper
Set of scripts used in the Lyve-SET paperani-m
Average Nucleotide Identity analysis with MUMmer under the hoodbio-js
Lee Katz's original bio-javascript libraryspaceballsTheFacemask
For EmmaportableBioinformatics
A set of toolslyve-MLST
A module for typing whole genomes, given a BigsDB-style MLST database.pp-file-magic
Pure perl file magiccronFileMoving
A sort of example repo for showing how to do automatic file copying safelyLove Open Source and this site? Check out how you can help us