Bioinformatics

• 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

Utilities

• csvtk, efficient and practical CSV/TSV toolkit
• rush, command-line tool for executing jobs in parallel
• brename, command-line tool for safely batch renaming

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