Lee Katz

mashtree. :deciduous_tree: Create a tree using Mash distances

awesome-bioinformatics-education. resources for bioinformatics education

fasten. :construction_worker: Fasten toolkit, for streaming operations on fastq files

awesome-bioinformatics-jobs. Resources for bioinformatics jobs

Kalamari. :octopus: A curated database of completed assemblies with taxonomy IDs

fundamentals-of-bioinformatics.

lyve-SET. :dancer: :palm_tree: 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.

adapterseqs. A repo with just adapter sequences

SneakerNet. :feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run

pdtk. NCBI Pathogen Detection Portal toolkit

CG-Pipeline. Genome assembly/prediction/annotation pipeline for the Linux command line

BookAI. Machine learning for making my novel

taxdb. Manipulate taxonomy databases

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

is-it-down.

dists2trees. Generic distances to trees pipeline

lskatz.github.io. Website for Lee Katz

hashest. estimate MLST with hashes

ani-m. Average Nucleotide Identity analysis with MUMmer under the hood

cgMLST-comparison. Jupyter Notebook

lyve-KSNP. a set of wrapper scripts for KSNP

file-find-fast. File::Find::Fast

template-perl. A simple template for perl projects

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

naughty-binfie-files. Shell

container-test. Test building containers

MLST-CLI. Make a database of wgMLST alleles and manipulate it

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

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

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

perl-app-hump. :camel: A perl module for workflow dependencies.

ubinfie.github.io. µbinfie blog

advent-of-code. https://adventofcode.com/

what3wordsRegion. Give a list of "what 3 words" for a region

ComputationalGenomicsManual. Robs manual for the computational genomics and bioinformatics class.

chowdown. Simple recipes in Markdown format

samclip. Filter SAM file for soft and hard clipped alignments

test-github-cache. Testing github actions caching

seqtk. Toolkit for processing sequences in FASTA/Q formats

taco-bell-locations. Print zip codes of taco bell locations.

adapter_benchmark. Benchmarking adapter and quality trimming tools

docker-builds. :package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

any2index. Perl

pp-file-magic. Pure perl file magic