jianshu93

Probabilistic data structures in Bioinformatics and Computational Biology. Collaboration with @jean-pierreBoth

University of California, San DiegoSan Diego

Pinned Repositories

adas
Advanced Database Search for Long Sequences
Language:Rust20
annembed
data embedding based on approximate nearest neighbour
Language:Rust1 0 00
bindash
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
Language:C++3 0 01
Competitive_mapping
Language:Shell2 2 30
dada2_wrapper
Language:R4 2 00
gsearch
Approximate nearest neighbour search for microbial genomes based on hash metric
Language:Rust4 0 01
hnswlib-rs
Rust implementation of the HNSW algorithm (Malkov-Yashunin)
Language:Rust1 1 00
hypermash
Fast and Memory Efficient Genome Sketching via HyperMinHash
Language:Rust50
kmerutils
Kmer generating, counting hashing and related
Language:Rust0 1 00
probminhash
Rust implementation of probminhash, superminhash and hyperloglog sketching algorithms
Language:Rust0 0 00

jianshu93's Repositories

jianshu93/hypermash
Fast and Memory Efficient Genome Sketching via HyperMinHash
Language:Rust50
jianshu93/gsearch
Approximate nearest neighbour search for microbial genomes based on hash metric
Language:Rust4 0 01
jianshu93/bindash
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
Language:C++3 0 01
jianshu93/adas
Advanced Database Search for Long Sequences
Language:Rust20
jianshu93/annembed
data embedding based on approximate nearest neighbour
Language:Rust1 0 00
jianshu93/finch-rs
A genomic minhashing implementation in Rust
Language:Rust1
jianshu93/hnswlib-rs
Rust implementation of the HNSW algorithm (Malkov-Yashunin)
Language:Rust1 1 00
jianshu93/annembed_analysis
reproducing scripts for annembed paper
Language:R1 0
jianshu93/annembed_gsearch
annembed old version for gsearch integration
Language:Rust
jianshu93/arrow-rs
Official Rust implementation of Apache Arrow
jianshu93/astar-pairwise-aligner
A pairwise sequence aligner written in Rust
Language:Rust1 0
jianshu93/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell0 0
jianshu93/blog
Build a Jekyll blog in minutes, without touching the command line.
Language:SCSS0 0
jianshu93/graphembed
graph embedding, density friendly decomposition
Language:Jupyter Notebook0 0
jianshu93/graphembed-analysis
Repo for analyzing graphembed crate
1 0
jianshu93/GreedyMini
jianshu93/homebrew-annembed
homebrew release for annembed
Language:Ruby1 0
jianshu93/JianshuZhao-website
Minimalist Hugo template for academic websites
jianshu93/matchms
Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.
jianshu93/mdmcleaner
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
Language:Python
jianshu93/minimap2-rs
Language:Rust0 0
jianshu93/minimap2-rs-test
Testing minimap2-rs for large-scale sequence alignment
Language:Rust
jianshu93/minimizers
Measure experimental density of bd-anchors
Language:Rust0 0
jianshu93/mzdata
Language:Rust
jianshu93/Nonredun
metagenomic coverage estimation for long and accurate reads
Language:R1 0
jianshu93/pangenome-visualization
visualization tool for pangenome
Language:Python
jianshu93/PhyloDM
Efficient calculation of phylogenetic distance matrices.
Language:Rust
jianshu93/sam_filter
Filter SAM file by sequence identity and alignment ratio
Language:Rust
jianshu93/sufr
Parallel Construction of Suffix Arrays in Rust
jianshu93/WITCH
WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.