| 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
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
