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LexicMap: efficient sequence alignment against millions of prokaryotic genomes​
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LexicMap

Latest Version Anaconda Cloud Cross-platform license

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.

Introduction

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
Installation Releases

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
Tutorials Usages FAQs

Accurate and efficient alignment

Using LexicMap to search in the whole 2,340,672 Genbank+Refseq prokaryotic genomes with 48 CPUs.

Query Genome hits Time RAM
A 1.3-kb marker gene 41,718 3m:09s 3.84GB
A 1.5-kb 16S rRNA 1,955,160 37m:52s 10.82GB
A 52.8-kb plasmid 561,717 51m:59s 13.96GB
1003 AMR genes 30,938,862 23h:13m:35s 22.5GB

Blastn is unable to run with the same dataset on common servers as it requires >2000 GB RAM.