lexicmap

name	lexicmap
description	LexicMap — efficient nucleotide alignment of moderate-length queries (genes, plasmids, long reads; typically >250 bp) against up to millions of prokaryotic genomes. Use when: (1) Searching genes/plasmids vs huge genome databases, (2) Scaling beyond BLAST/minimap2 for AllTheBacteria / GTDB-scale refs, (3) Epidemiology/ecology queries needing fast genome hits. Upstream: https://github.com/shenwei356/LexicMap. Not a substitute for short-read→contig coverage mappers (strobealign/bowtie2) used in binning.
license	MIT
category	analysis-tools
tags	["alignment","search","LexicMap","genomes","BLAST"]
upstream	https://github.com/shenwei356/LexicMap
stage	mapping

LexicMap

Upstream: shenwei356/LexicMap

Citation

Shen, W., Lees, J. A. & Iqbal, Z. Efficient sequence alignment against millions of prokaryotic genomes with LexicMap. Nat. Biotechnol. (2025). https://doi.org/10.1038/s41587-025-02812-8

See also docs/references.md.

Analytical thinking

Problem: BLAST-style search against millions of bacterial genomes. LexicMap indexes probe/seed structure for fast, lower-memory alignment of moderate-length queries. Use for gene/plasmid/long-read queries against large genome warehouses (progenomes, AllTheBacteria, GTDB reps).

Task	Prefer
Illumina reads → contigs (binning coverage)	strobealign / bowtie2
Gene/plasmid vs million genomes	lexicmap
Phylogeny-compressed 661k on a laptop	phylign
Protein remote homology	diamond / mmseqs2 / erast
Species ANI between MAGs	skani / fastani

How to run

# build index once; query many times — see upstream docs
lexicmap index -d genomes_dir -o db/lexicmap_idx
lexicmap search -d db/lexicmap_idx -q query.fa -o temp/lexicmap/hits.tsv

Related skills

homology-search · phylign · minimap2 · diamond · mmseqs2 · erast · progenomes · gtdb · plasmaag · tool-selection