Jung Soo Lee's repositories
bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
CHM13
The complete sequence of a human genome
comprehensive-rust
This is the Rust course used by the Android team at Google. It provides you the material to quickly teach Rust to everyone.
deeplearning4j
Suite of tools for deploying and training deep learning models using the JVM. Highlights include model import for keras, tensorflow, and onnx/pytorch, a modular and tiny c++ library for running math code and a java based math library on top of the core c++ library. Also includes samediff: a pytorch/tensorflow like library for running deep learning
deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
DRAGMAP
DRAGEN open-source mapper
freebayes
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
JslCodes
Toy codes that I upload
jslfree080
My github profile
MyWebsite
https://www.jslfree080.com
practicetsne
Play around with various datasets using t-SNE on my own.
YouPlot
A command line tool that draw plots on the terminal.
GenPipes
GenPipes Read the Docs repository
jbrowse-components
Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.
minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
nanofilt
Filtering and trimming of long read sequencing data
Porechop
adapter trimmer for Oxford Nanopore reads
ruby-htslib
HTSlib bindings for Ruby
seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
Sniffles
Structural variation caller using third generation sequencing