Pinned Repositories
awesome-bioinformatics-education
resources for bioinformatics education
awesome-bioinformatics-jobs
Resources for bioinformatics jobs
fasten
:construction_worker: Fasten toolkit, for streaming operations on fastq files
Kalamari
:octopus: A curated database of completed assemblies with taxonomy IDs
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.
lyve-SET
:dancer: :palm_tree: LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
mashtree
:deciduous_tree: Create a tree using Mash distances
pdtk
NCBI Pathogen Detection Portal toolkit
SneakerNet
:feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
mashpit
:pencil: Sketch-based surveillance platform
lskatz's Repositories
lskatz/mashtree
:deciduous_tree: Create a tree using Mash distances
lskatz/fasten
:construction_worker: Fasten toolkit, for streaming operations on fastq files
lskatz/awesome-bioinformatics-education
resources for bioinformatics education
lskatz/Kalamari
:octopus: A curated database of completed assemblies with taxonomy IDs
lskatz/awesome-bioinformatics-jobs
Resources for bioinformatics jobs
lskatz/lyve-SET
:dancer: :palm_tree: LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
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.
lskatz/SneakerNet
:feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
lskatz/pdtk
NCBI Pathogen Detection Portal toolkit
lskatz/CG-Pipeline
Genome assembly/prediction/annotation pipeline for the Linux command line
lskatz/mlst-hash-template
This is a template for any new hash-based MLST database
lskatz/lskatz.github.io
Website for Lee Katz
lskatz/advent-of-code
https://adventofcode.com/
lskatz/file-find-fast
File::Find::Fast
lskatz/nextflow-perl
a very superficial attempt to replace nextflow's java engine with perl
lskatz/perl-app-hump
:camel: A perl module for workflow dependencies.
lskatz/Schedule--SGELK
Perl module for scheduling tasks, with only using qsub/qstat/qdel. A very portable scheduler.
lskatz/any2index
lskatz/Bio--Kmer
A perl module for kmer counting
lskatz/chowdown
Simple recipes in Markdown format
lskatz/ROSS
ROSS - Random Operations on Sequences Suite
lskatz/what3wordsRegion
Give a list of "what 3 words" for a region
lskatz/bioconda-recipes
Conda recipes for the bioconda channel.
lskatz/Email-Stuffer
for sending stuff through email
lskatz/gfa-parser
Toy project for parsing GFA in perl
lskatz/make-perl-code-faster
Born again "perl-benchmark-collection" repository
lskatz/perl-benchmark-collection
My perl benchmark scripts
lskatz/primerForge
software to identify primers that can distinguish genomes
lskatz/spark
▁▂▃▅▂▇ in your shell.
lskatz/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks