jianshu93

jianshu93's Stars

• simdjson/simdjson

  Parsing gigabytes of JSON per second : used by Facebook/Meta Velox, the Node.js runtime, ClickHouse, WatermelonDB, Apache Doris, Milvus, StarRocks

  Language:C++19.6k2428501k

• simd-lite/simd-json

  Rust port of simdjson

  Language:Rust1.2k1815684

• SunPengChuan/wgdi

  WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

  Language:Python13035023

• biobakery/Maaslin2

  MaAsLin2: Microbiome Multivariate Association with Linear Models

  Language:R12982135

• IndexThePlanet/Logan

  Logan Unitigs and Contigs

  1118133

• chasewnelson/SNPGenie

  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

  Language:Perl110107637

• unageek/graphest

  A faithful graphing calculator

  Language:Rust1022301

• bcgsc/ntEdit

  ✏️ Genome assembly polishing & SNV detection

  Language:C++6414199

• 5cript/interval-tree

  A C++ header only interval tree implementation.

  Language:C++6381914

• moshi4/COGclassifier

  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

  Language:Python59216

• mourisl/centrifuger

  Classifier for metagenomic sequences using FM-index with run-block compressed BWT.

  Language:C++523124

• yunwilliamyu/hyperminhash

  LogLog space version of MinHash by combining ideas from HyperLogLog and b-bit MinHash

  Language:Python51538

• CMU-SAFARI/RawHash

  RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).

  Language:C508105

• RabbitBio/RabbitTClust

  RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

  Language:C++453134

• bluenote-1577/fairy

  alignment-free coverage calculation for metagenomic binning >100 times faster

  Language:Rust39271

• martinjrobins/diffsol

  ODE solver library in Rust

  Language:Rust374404

• kcleal/pywfa

  Python wrapper for wavefront alignment using WFA2-lib

  Language:Python355133

• prophyle/prophasm

  ProphAsm – a rapid computation of simplitigs directly from k-mer sets

  Language:C++262116

• ocxtal/dozeu

  SIMD-parallel BLAST X-drop DP on sequence graphs

  Language:C24617

• ChrisCreevey/catsequences

  A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses

  Language:C20215

• pesho-ivanov/minSH

  A minimal Python re-implementation of the A* with seed heuristic for exact global alignment (edit distance) in near-linear time

  Language:Jupyter Notebook20307

• hcho3/skiplist_cuda

  A parallel (CUDA) implementation of skiplist

  Language:Cuda14304

• chasewnelson/OLGenie

  Program for estimating dN/dS in overlapping genes (OLGs)

  Language:Perl13252

• vicLeva/bqf

  Implementation of a Backpack Quotient Filter

  Language:C++11110

• ucrparlay/Edit-Distance

  ESA'23: Efficient Parallel Output-Sensitive Edit Distance

  Language:C++10511

• natir/knot

  KNOT: Knowledge Network Overlap exTraction is a tool for the investigation of fragmented long read assemblies.

  Language:HTML521

• ARU-life-sciences/extract_nhmmer_tblout

  Get the nhmmer identified sequences back from a FASTA file.

  Language:Rust1020

• ctb/pp-sketchlib

  Library of sketching functions used by PopPUNK

  Language:C++100

• lukaslueg/pyhyperminhash

  Very fast, constant memory-footprint cardinality approximation, including intersection and union operation.

  Language:Rust120

• LukeMathWalker/googletest-rust

  Language:Rust100