shenwei356/blast-nf

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Language Nextflow
License
MIT License
Created over 5 years ago
Updated over 4 years ago

shenwei356/blast-nf

shenwei356

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A nextflow-based BLAST command-line helper tool

seqkit

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

csvtk

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

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

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

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.