lskatz/SneakerNet

Stars
12
Rank 1,597,372 (Top 32 %)
Language
Perl
License
Apache License 2.0
Created over 8 years ago
Updated over 1 year ago

lskatz/SneakerNet

lskatz

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

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.

pdtk

NCBI Pathogen Detection Portal toolkit

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

dists2trees

Generic distances to trees pipeline

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/

cecaelia

Earmarking a tool that would read kraken raw output and detect chimera reads or contigs

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

Suffix--trie

Pure Perl suffix trie

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

test-github-cache

Testing github actions caching

sha256emoji

Create an emoji hashsum from a file

Bio--Kmer

A perl module for kmer counting

biophp-at-ga-tech

Bioinformatics tools for PHP

template-perl

A simple template for perl projects

Schedule--SGELK

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

callsam

Call variants on sam files

biophp

Lee Katz's BioPHP

taco-bell-locations

Print zip codes of taco bell locations.

any2index

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