Jianshu_Zhao's repositories
phyloFlash
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
usearch_wrapper
usearch wrapper for amplicon analysis. Support for 16S and ITS
amadeus
Harmonious distributed data analysis in Rust.
bakta
Rapid & standardized annotation of bacterial genomes & plasmids
ball-tree
A ball-tree implementation for K-NN
bam-readcount
count DNA sequence reads in BAM files
daggy
A directed acyclic graph data structure for Rust.
finch-rs
A genomic minhashing implementation in Rust
flann
Fast Library for Approximate Nearest Neighbors
gfabase
GFA insert into GenomicSQLite
goalign
Goalign is a set of command line tools and an API to manipulate multiple alignments. It is implemented in Go language.
granne
Graph-based Approximate Nearest Neighbor Search
graphalgs
Graph algorithms based on the Rust "petgraph" library.
jianshu93.github.io
personal website
LRA
Long read aligner
lsh-rs
Locality Sensitive Hashing in Rust with Python bindings
MAG_tools
self written MAG analysis tools
metagraph
Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
mOTUlizer
Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin
niffler
Simple and transparent support for compressed files.
orthoani
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
OrtSuite
Prediction of microbial interactions in complex communities
piz-rs
Parallelized zip archive reading
rs-gfa
GFA parser in Rust
rust-debruijn
De Bruijn graphs in Rust
spacegraphcats
Indexing large assembly graphs -- remember, in space, no one can hear you miao!
speedyseq
Speedy versions of phyloseq functions
SPTAG
A distributed approximate nearest neighborhood search (ANN) library which provides a high quality vector index build, search and distributed online serving toolkits for large scale vector search scenario.
triple_accel
Rust edit distance routines accelerated using SIMD. Supports fast Hamming, Levenshtein, restricted Damerau-Levenshtein, etc. distance calculations and string search.
vcxproj2makefile
Simple python2 script to convert Microsoft Visual Studio C++ project to gcc Makefile