lskatz

CDC (work) + personal projectsAtlanta, GA

Pinned Repositories

awesome-bioinformatics-education
resources for bioinformatics education
76 3 410
awesome-bioinformatics-jobs
Resources for bioinformatics jobs
35 3 22
fasten
:construction_worker: Fasten toolkit, for streaming operations on fastq files
Language:Rust77 5 166
Kalamari
:octopus: A curated database of completed assemblies with taxonomy IDs
Language:Perl39 6 303
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.
Language:Perl17 7 213
lyve-SET
:dancer: :palm_tree: LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
Language:Perl25 12 7018
mashtree
:deciduous_tree: Create a tree using Mash distances
Language:Perl157 13 8225
pdtk
NCBI Pathogen Detection Portal toolkit
Language:Perl11 2 10
SneakerNet
:feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
Language:Perl11 5 504
mashpit
:pencil: Sketch-based surveillance platform
Language:Python9 4 204

lskatz's Repositories

lskatz/fasten
:construction_worker: Fasten toolkit, for streaming operations on fastq files
Language:Rust77 5 166
lskatz/awesome-bioinformatics-education
resources for bioinformatics education
76 3 410
lskatz/Kalamari
:octopus: A curated database of completed assemblies with taxonomy IDs
Language:Perl39 6 303
lskatz/awesome-bioinformatics-jobs
Resources for bioinformatics jobs
35 3 22
lskatz/lyve-SET
:dancer: :palm_tree: LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
Language:Perl25 12 7018
lskatz/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.
Language:Perl17 7 213
lskatz/SneakerNet
:feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
Language:Perl11 5 504
lskatz/CG-Pipeline
Genome assembly/prediction/annotation pipeline for the Linux command line
Language:Perl8 5 42
lskatz/mlst-hash-template
This is a template for any new hash-based MLST database
Language:Perl5 2 252
lskatz/dists2trees
Generic distances to trees pipeline
Language:Perl4 2 2
lskatz/lskatz.github.io
Website for Lee Katz
Language:JavaScript4 3 01
lskatz/advent-of-code
https://adventofcode.com/
Language:Perl2 3 0
lskatz/cecaelia
Earmarking a tool that would read kraken raw output and detect chimera reads or contigs
Language:Perl2 1 0
lskatz/file-find-fast
File::Find::Fast
Language:Perl2 2 0
lskatz/nextflow-perl
a very superficial attempt to replace nextflow's java engine with perl
Language:Perl2 3 1
lskatz/Schedule--SGELK
Perl module for scheduling tasks, with only using qsub/qstat/qdel. A very portable scheduler.
Language:Perl2 3 11
lskatz/ubinfie.github.io
µbinfie blog
Language:HTML2 1 0
lskatz/Bio--Kmer
A perl module for kmer counting
Language:Perl1 3 73
lskatz/chowdown
Simple recipes in Markdown format
Language:HTML1 1 0
lskatz/samclip
Filter SAM file for soft and hard clipped alignments
1
lskatz/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell1 0
lskatz/inara
Tools to create JOSS/JOSE publishing artifacts
Language:Lua0 0
lskatz/make-perl-code-faster
Born again "perl-benchmark-collection" repository
Language:Perl2 0
lskatz/mlst-hash-experiment
experiments in hash collisions
Language:Perl
lskatz/perl-benchmark-collection
My perl benchmark scripts
Language:Perl
lskatz/primerForge
software to identify primers that can distinguish genomes
Language:Python1 0
lskatz/semver
Semantic Versioning Specification
0 0
lskatz/spark
▁▂▃▅▂▇ in your shell.
Language:Shell3 0
lskatz/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
Language:Python1 0
lskatz/test-datasets
Test data to be used for automated testing with the nf-core pipelines