Lee Katz (@lskatz)

Top repositories

1

mashtree

🌳 Create a tree using Mash distances
Perl
136
star
2

fasten

πŸ‘· Fasten toolkit, for streaming operations on fastq files
Rust
75
star
3

awesome-bioinformatics-education

resources for bioinformatics education
63
star
4

Kalamari

πŸ™ A curated database of completed assemblies with taxonomy IDs
Perl
38
star
5

awesome-bioinformatics-jobs

Resources for bioinformatics jobs
31
star
6

lyve-SET

πŸ’ƒ 🌴 LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
Perl
23
star
7

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.
Perl
15
star
8

SneakerNet

🐾 QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
Perl
12
star
9

pdtk

NCBI Pathogen Detection Portal toolkit
Perl
9
star
10

CG-Pipeline

Genome assembly/prediction/annotation pipeline for the Linux command line
Perl
7
star
11

annapotater

Quick and dirty SNP annotator
Perl
5
star
12

mlst-hash-template

This is a template for any new hash-based MLST database
Perl
5
star
13

is-it-down

4
star
14

BookAI

Machine learning for making my novel
Perl
4
star
15

taxdb

Manipulate taxonomy databases
Perl
4
star
16

lskatz.github.io

Website for Lee Katz
JavaScript
4
star
17

lyve-KSNP

a set of wrapper scripts for KSNP
Shell
3
star
18

hashest

estimate MLST with hashes
Perl
3
star
19

cgMLST-comparison

Jupyter Notebook
3
star
20

naughty-binfie-files

Shell
2
star
21

container-test

Test building containers
Dockerfile
2
star
22

file-find-fast

File::Find::Fast
Perl
2
star
23

advent-of-code

https://adventofcode.com/
Perl
2
star
24

hash2seq

Given a reference sequence and a hash, reverse engineer what the sequence is
Perl
2
star
25

MLST-CLI

Make a database of wgMLST alleles and manipulate it
Perl
2
star
26

readTaxonomy

Methods in various languages for how to create a fast database from NCBI Taxonomy
Perl
2
star
27

perl-app-hump

🐫 A perl module for workflow dependencies.
Perl
2
star
28

nextflow-perl

a very superficial attempt to replace nextflow's java engine with perl
Perl
2
star
29

SARS-CoV-2-trueTree

True tree for a SARS-CoV-2 phylogeny
1
star
30

ROSS

ROSS - Random Operations on Sequences Suite
Perl
1
star
31

perl-mash

perl module for Mash sketches
Perl
1
star
32

template-perl

A simple template for perl projects
Perl
1
star
33

test-github-cache

Testing github actions caching
1
star
34

Bio--Kmer

A perl module for kmer counting
Perl
1
star
35

Suffix--trie

Pure Perl suffix trie
Perl
1
star
36

sha256emoji

Create an emoji hashsum from a file
Rust
1
star
37

biophp-at-ga-tech

Bioinformatics tools for PHP
1
star
38

Schedule--SGELK

Perl module for scheduling tasks, with only using qsub/qstat/qdel. A very portable scheduler.
Perl
1
star
39

callsam

Call variants on sam files
Perl
1
star
40

any2index

Perl
1
star
41

biophp

Lee Katz's BioPHP
PHP
1
star
42

taco-bell-locations

Print zip codes of taco bell locations.
Perl
1
star
43

what3wordsRegion

Give a list of "what 3 words" for a region
Perl
1
star
44

ncbiClusters

Perl
1
star
45

Lyve-SET-paper

Set of scripts used in the Lyve-SET paper
Perl
1
star
46

ani-m

Average Nucleotide Identity analysis with MUMmer under the hood
Perl
1
star
47

bio-js

Lee Katz's original bio-javascript library
HTML
1
star
48

spaceballsTheFacemask

For Emma
Python
1
star
49

portableBioinformatics

A set of tools
JavaScript
1
star
50

lyve-MLST

A module for typing whole genomes, given a BigsDB-style MLST database.
Shell
1
star
51

pp-file-magic

Pure perl file magic
Perl
1
star
52

cronFileMoving

A sort of example repo for showing how to do automatic file copying safely
Shell
1
star