shenwei356/awesome

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shenwei356/awesome

shenwei356

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

awesome

Collection of useful resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl, etc.) and miscellaneous stuff.

Table of Contents

Technology
Programming languages
Specific domains
Miscellaneous
License

Technology

Programming languages

Specific domains

Bioinformatics

Miscellaneous

License

seqkit

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

csvtk

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

taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies

brename

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

kmcp

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

LexicMap

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

bio_scripts

Practical, reusable scripts for bioinformatics

bio

A lightweight and high-performance bioinformatics package in Golang

unikmer

Toolkit for k-mer with taxonomic information

ClipboardTextJoiner

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

go4bio

Golang for Bioinformatics

gtdb-taxdump

GTDB taxonomy taxdump files with trackable TaxIds

easy_qsub

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

countminsketch

An implementation of Count-Min Sketch in Golang

taxid-changelog

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

bwt

Burrows-Wheeler Transform and FM-index in golang

cnote

A platform independent command line note app

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.

easy_sbatch

easy_sbatch - Batch submitting Slurm jobs with script templates

ncbi_acc2gtdb_acc

Mapping NCBI Genbank accession to GTDB accession

strobemers

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

ictv-taxdump

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

crun

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

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

lexichash

LexicHash in Golang

pand

Bitwise AND on two byte-slices using SIMD instructions

unik

A k-mer serialization package for Golang

kmers

bit-packed k-mers methods for Golang

install-windows

Windows系统安装经验

perfect-bioinformatic-tools

What should perfect bioinformatic tools be like?

breseq-rm-bg

Removing control/background mutations from breseq output index.html

bbuffer

An alternative of standard library bytes.Buffer

dirsize

Summarize size of directories and files in directories

datakit

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

util

Golang utility packages

uint64-hash-bench

Benchmark of three uint64 hash functions

simhash-eval

sun2021-cami-profiles

Ground truth metagenomic profiles in CAMI format for the 25 metagenomic reads in Sun et al.

go-hashing-kmer-bench

Benchmark of hashing k-mers in Golang

shenwei356

RNA-HairpinFigure

Draw hairpin-like text figure from RNA sequence and its secondary structure in dot-bracket notation.

BioUtil

Bioinformatics Perl modules

rust-practice

Some tools in Rust for learning

todo

A very simple online todo list application

blast-nf

A nextflow-based BLAST command-line helper tool

easy_run

Run command with default options in configuration file

swr

Wei Shen' R utilities

shenwei356.github.io

uintset

Fast uint64 Set in golang

process_queue

Process queue for high CPU/RAM/time usage processes

roux2016-mock-virome-cami-profile

Ground truth metagenomic profiles in CAMI format for the mock virome communities in Roux et al.