LexicMap
LexicMap is a nucleotide sequence alignment tool for efficiently querying gene, plasmid, virus, or long-read sequences (>100 bp) against up to millions of prokaryotic genomes.
Feature overview
Easy to install
Linux, Windows, MacOS and more OS are supported.
Both x86 and ARM CPUs are supported.
Just download the binary files and run!
Or install it by
conda install -c bioconda lexicmap
Easy to use
Step 1: indexing
lexicmap index -I genomes/ -O db.lmi
Step 2: searching
lexicmap search -d db.lmi q.fasta -o r.tsv
Accurate and efficient alignment
Using LexicMap to align in the whole 2,340,672 Genbank+Refseq prokaryotic genomes with 48 CPUs.
| Query | Genome hits | Time | RAM(GB) |
|---|---|---|---|
| A 1.3-kb gene | 41,718 | 3m:06s | 3.97 |
| A 1.5-kb 16S rRNA | 1,955,167 | 32m:59s | 11.09 |
| A 52.8-kb plasmid | 560,330 | 52m:22s | 14.48 |
| 1003 AMR genes | 30,967,882 | 15h:52m | 24.86 |
Blastn is unable to run with the same dataset on common servers as it requires >2000 GB RAM.