lskatz/pdtk

Stars
9
Rank 1,900,035 (Top 39 %)
Language
Perl
License
MIT License
Created 10 months ago
Updated 10 months ago

lskatz/pdtk

lskatz

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NCBI Pathogen Detection Portal toolkit

mashtree

🌳 Create a tree using Mash distances

fasten

👷 Fasten toolkit, for streaming operations on fastq files

awesome-bioinformatics-education

resources for bioinformatics education

Kalamari

🐙 A curated database of completed assemblies with taxonomy IDs

awesome-bioinformatics-jobs

Resources for bioinformatics jobs

lyve-SET

💃 🌴 LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations

lskScripts

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.

SneakerNet

🐾 QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run

CG-Pipeline

Genome assembly/prediction/annotation pipeline for the Linux command line

annapotater

Quick and dirty SNP annotator

mlst-hash-template

This is a template for any new hash-based MLST database

is-it-down

BookAI

Machine learning for making my novel

taxdb

Manipulate taxonomy databases

lskatz.github.io

Website for Lee Katz

lyve-KSNP

a set of wrapper scripts for KSNP

hashest

estimate MLST with hashes

cgMLST-comparison

Jupyter Notebook

naughty-binfie-files

container-test

Test building containers

file-find-fast

File::Find::Fast

advent-of-code

https://adventofcode.com/

hash2seq

Given a reference sequence and a hash, reverse engineer what the sequence is

MLST-CLI

Make a database of wgMLST alleles and manipulate it

readTaxonomy

Methods in various languages for how to create a fast database from NCBI Taxonomy

perl-app-hump

🐫 A perl module for workflow dependencies.

nextflow-perl

a very superficial attempt to replace nextflow's java engine with perl

SARS-CoV-2-trueTree

True tree for a SARS-CoV-2 phylogeny

ROSS

ROSS - Random Operations on Sequences Suite

perl-mash

perl module for Mash sketches

template-perl

A simple template for perl projects

test-github-cache

Testing github actions caching

Bio--Kmer

A perl module for kmer counting

Suffix--trie

Pure Perl suffix trie

sha256emoji

Create an emoji hashsum from a file

biophp-at-ga-tech

Bioinformatics tools for PHP

Schedule--SGELK

Perl module for scheduling tasks, with only using qsub/qstat/qdel. A very portable scheduler.

callsam

Call variants on sam files

any2index

biophp

Lee Katz's BioPHP

taco-bell-locations

Print zip codes of taco bell locations.

what3wordsRegion

Give a list of "what 3 words" for a region

ncbiClusters

Lyve-SET-paper

Set of scripts used in the Lyve-SET paper

ani-m

Average Nucleotide Identity analysis with MUMmer under the hood

bio-js

Lee Katz's original bio-javascript library

spaceballsTheFacemask

portableBioinformatics

lyve-MLST

A module for typing whole genomes, given a BigsDB-style MLST database.

pp-file-magic

Pure perl file magic

cronFileMoving

A sort of example repo for showing how to do automatic file copying safely