Wei Shen

seqkit. A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

csvtk. A cross-platform, efficient and practical CSV/TSV toolkit in Golang

rush. A cross-platform command-line tool for executing jobs in parallel

awesome. Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.

taxonkit. A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

brename. A practical cross-platform command-line tool for safely batch renaming files/directories via regular expression

LexicMap. LexicMap: efficient sequence alignment against millions of prokaryotic genomes

kmcp. Accurate metagenomic profiling && Fast large-scale sequence/genome searching

perfect-bioinformatic-tools. What should perfect bioinformatic tools be like?

bio_scripts. Practical, reusable scripts for bioinformatics

bio. A lightweight and high-performance bioinformatics package in Golang

BlackheartedHospital. 网传附莆田系医院名单，欢迎更新

unikmer. A versatile toolkit for k-mers with taxonomic information

gtdb-taxdump. GTDB taxonomy taxdump files with trackable TaxIds

ClipboardTextJoiner. Monitoring system clipboard change and joining multi-line text. It's very useful when copying multi-line text from PDF files.

countminsketch. An implementation of Count-Min Sketch in Golang

go4bio. Golang for Bioinformatics

wfa. Wavefront alignment algorithm (WFA) in Golang

easy_qsub. Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.

taxid-changelog. NCBI taxonomic identifier (taxid) changelog, including taxids deletion, new adding, merge, reuse, and rank/name changes.

ictv-taxdump. NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)

bwt. Burrows-Wheeler Transform and FM-index in golang

memusg. A 'time'-like utility for Unix that measures peak memory usage

cnote. A platform independent command line note app

easy_sbatch. easy_sbatch - Batch submitting Slurm jobs with script templates

gtaxon. gTaxon - a fast cross-platform NCBI taxonomy data querying (gi2taxid, taxid2taxon, name2taxid, LCA) tool, with cmd client and REST API server for both local and remote server.

ncbi_acc2gtdb_acc. Mapping NCBI Genbank accession to GTDB accession

strobemers. A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)

stable. Streaming pretty text table for Golang

crun. Run workflow mixed with concurrent and sequential jobs. Please use https://github.com/shenwei356/rush

kmers. bit-packed k-mers methods for Golang

pand. Bitwise AND on two byte-slices using SIMD instructions

breader. breader (Buffered File Reader), asynchronous parsing and pre-processing while reading file. Safe cancellation is also supported.

pinyin. 收集汉字，结合汉语拼音来取名

unik. A k-mer serialization package for Golang

lexichash. LexicHash in Golang

install-windows. Windows系统安装经验

Awesome-Bioinformatics. A curated list of awesome Bioinformatics libraries and software.

bbuffer. An alternative of standard library bytes.Buffer

dirsize. Summarize sizes of directories and files in directories

breseq-rm-bg. Removing control/background mutations from breseq output index.html

datakit. CSV/TSV file manipulation and more. Please use my another tool: csvtk, https://github.com/shenwei356/csvtk

rust-practice. Some tools in Rust for learning

util. Golang utility packages

lexicmap-benchmark. R

biofast. Benchmarking programming languages/implementations for common tasks in Bioinformatics

go-hashing-kmer-bench. Benchmark of hashing k-mers in Golang

cluster_files. cluster files into multiple directories by creating symbolic links or moving files

uint64-hash-bench. Benchmark of three uint64 hash functions

shenwei356.

seqkit2_benchmark. Shell

simhash-eval. Go

genome_updater. Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

cami2_pipelines. assembly, binning, profiling pipelines for CAMI2