Bioinformatics

Tools:

• LexicMap, efficient sequence alignment against millions of prokaryotic genomes
• KMCP, accurate metagenomic profiling && fast large-scale sequence/genome searching
• SeqKit, fast and versatile toolkit for FASTA/Q file
• TaxonKit, practical and efficient NCBI Taxonomy toolkit
• unikmer, toolkit for nucleic acid k-mer analysis

Data:

• taxid-changelog, NCBI taxonomic identifier (taxid) changelog, including taxids deletion, new adding, merge, reuse, and rank/name changes.
• gtdb-taxdump and ictv-taxdump, GTDB and ICTV taxonomy taxdump files with trackable TaxIds

Packages:

• bio, A lightweight and high-performance bioinformatics package in Golang.
  • FASTA/Q reading
  • Sketching algorithms, including Minimizer, Protein Minimizer, Scaled MinHash, Closed Syncmers
  • Taxonomy data manipulation
• kmers, Bit-packed k-mers methods for Golang
• unik, A k-mer serialization package for Golang
• lexichash, LexicHash in Golang
• wfa, Wavefront alignment algorithm (WFA) in Golang
• strobemers, A Go implementation of the strobemers
• bwt, Burrows-Wheeler Transform and FM-index in Golang
• countminsketch, Count-Min Sketch in Golang

Utilities

Tools:

• csvtk, efficient and practical CSV/TSV toolkit
• rush, command-line tool for executing jobs in parallel
• brename, command-line tool for safely batch renaming
• cluster_files, organizing (FASTQ) files for parallel analysis
• dirsize, summarize sizes of directories and files in directories

Packages:

• stable, streaming pretty text table for Golang

Others

• perfect-bioinformatic-tools, suggestions for improving the usability of bioinformatic (command-line) tools

Retired software

• FOMmiR, MicroRNA Prediction Using a Fixed-Order Markov Model Based on the Secondary Structure Pattern
• Fastcov, A novel algorithm for detecting multiple covariance and clustering of biological sequences