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‎CHANGELOG.md‎

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# Changelog
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### v0.8.0 - 2025-xx-xx
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### v0.8.0 - 2025-09-10
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No changes to the index format (see [Index format changelog](https://bioinf.shenwei.me/LexicMap/tutorials/index/#index-format-changelog)).
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- New commands:
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- **`lexicmap utils merge-search-results`: Merge a query's search results from multiple indexes**.

‎README.md‎

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## <a href="https://bioinf.shenwei.me/LexicMap"><img src="logo.svg" width="30"/></a> LexicMap: efficient sequence alignment against millions of prokaryotic genomes​
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## <a href="https://bioinf.shenwei.me/LexicMap"><img src="logo.svg" width="36"/></a> LexicMap: efficient sequence alignment against millions of prokaryotic genomes​
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[![Latest Version](https://img.shields.io/github/release/shenwei356/LexicMap.svg?style=flat?maxAge=86400)](https://github.com/shenwei356/LexicMap/releases)
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[![Anaconda Cloud](https://anaconda.org/bioconda/lexicmap/badges/version.svg)](https://anaconda.org/bioconda/lexicmap)
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For the latest features and improvements, please download the [pre-release binaries](https://github.com/shenwei356/LexicMap/issues/10).
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Preprint:
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Please cite:
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> Wei Shen, John A. Lees, Zamin Iqbal.
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> (2024) LexicMap: efficient sequence alignment against millions of prokaryotic genomes.
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> bioRxiv. [https://doi.org/10.1101/2024.08.30.610459](https://doi.org/10.1101/2024.08.30.610459)
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> (2025) Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.
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> Nature Biotechnology. [https://doi.org/10.1038/s41587-025-02812-8](https://doi.org/10.1038/s41587-025-02812-8)
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## Table of contents
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- [ LexicMap: efficient sequence alignment against millions of prokaryotic genomes​](#-lexicmap-efficient-sequence-alignment-against-millions-of-prokaryotic-genomes)
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- [Table of contents](#table-of-contents)
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- [Features](#features)
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- [Introduction](#introduction)
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- [Quick start](#quick-start)
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## Features
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1. **The accuracy of LexicMap is comparable with Blastn, MMseqs2, and Minimap2**. It
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- performs **base-level alignment**, with `qcovGnm`, `qcovHSP`, `pident`, `evalue` and `bitscore` returned,
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- **performs base-level alignment**, with `qcovGnm`, `qcovHSP`, `pident`, `evalue` and `bitscore` returned,
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both in TSV and pairwise alignment format ([output format](https://bioinf.shenwei.me/LexicMap/tutorials/search/#output)).
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- provides a genome-wide query coverage metric (`qcovGnm`),
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which enables accurate interpretation of search results - particularly for [circular queries (such as plasmid, virus, and mtDNA)](https://bioinf.shenwei.me/LexicMap/tutorials/search/#searching-with-plasmids-or-other-longer-queries)
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against both complete and fragmented assemblies.
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- returns all possible matches, including multiple copies of a gene in a genome.
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- **returns all possible matches**, including multiple copies of a gene in a genome.
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1. **The alignment is fast and memory-efficient, scalable to up to millions of prokaryotic genomes**.
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1. LexicMap is **easy to [install](http://bioinf.shenwei.me/LexicMap/installation/),
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we provide [binary files](https://github.com/shenwei356/LexicMap/releases/)** with no dependencies for Linux, Windows, MacOS (x86 and arm CPUs).
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2. LexicMap is **easy to use** (see [tutorials](http://bioinf.shenwei.me/LexicMap/tutorials/index/), [usages](http://bioinf.shenwei.me/LexicMap/usage/lexicmap/), and [FAQs](https://bioinf.shenwei.me/LexicMap/faqs/)).
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- [Database building](https://bioinf.shenwei.me/LexicMap/tutorials/index/) requires only a simple command, accepting input from files, a file list, or even a directory.
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- [Sequence searching](https://bioinf.shenwei.me/LexicMap/tutorials/search/) supports limiting search by TaxId(s), provides a progress bar.
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- [Several utility commands](https://bioinf.shenwei.me/LexicMap/usage/utils/) are available to resume unfinished indexing, and explore the index data, extract indexed subsequences.
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- [Several utility commands](https://bioinf.shenwei.me/LexicMap/usage/utils/) are available to resume unfinished indexing, explore the index data, merge search results, extract matched subsequences and more.
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## Introduction
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1. LexicMap enables efficient indexing and searching of both RefSeq+GenBank and the [AllTheBacteria](https://www.biorxiv.org/content/10.1101/2024.03.08.584059v1) datasets (**2.3 and 1.9 million prokaryotic assemblies** respectively).
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1. When searching in all **2,340,672 Genbank+Refseq prokaryotic genomes**, *Blastn is unable to run with this dataset on common servers as it requires >2000 GB RAM*. (see [performance](#performance)).
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**With LexicMap v0.7.0** (48 CPUs),
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**With LexicMap v0.7.0** (48 CPUs, indexes and queries queries in HDDs),
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|Query |Genome hits|Genome hits<br/>(high-similarity)|Genome hits<br/>(medium-similarity)|Genome hits<br/>(low-similarity)|Time |RAM |
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|:-------------------|----------:|--------------------------------:|----------------------------------:|-------------------------------:|----------:|-------:|
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1. Only the best alignment of a genome is used to evaluate alignment similarity:
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- high-similarity: (a) qcov >= 90% (genes) or 70% (plasmids), (b) pident>=90%.
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- medium-similarity: (a) not belong to high-similarity, (b) qcov >= 50% (genes) or 30% (plasmids), (c) pident>=80%.
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- low-similarity: left.
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1. The search time varies in different computing environments and mainly depends on the I/O speed.
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- low-similarity: the remaining.
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1. The search time varies in different computing environments and mainly depends on the I/O speed and the number of threads.
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More documents: https://bioinf.shenwei.me/LexicMap.
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## Citation
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> Wei Shen, John A. Lees, Zamin Iqbal.
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> (2024) LexicMap: efficient sequence alignment against millions of prokaryotic genomes.
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> bioRxiv. [https://doi.org/10.1101/2024.08.30.610459](https://doi.org/10.1101/2024.08.30.610459)
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> (2025) Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.
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> Nature Biotechnology. [https://doi.org/10.1038/s41587-025-02812-8](https://doi.org/10.1038/s41587-025-02812-8)
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## Limitations
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‎docs/content/_index.md‎

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lexicmap search -d db.lmi q.fasta -o r.tsv
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[10 utility commands](https://bioinf.shenwei.me/LexicMap/usage/utils/) are available
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to explore the index data, merge search results, extract matched subsequences and more.
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{{< button size="small" relref="tutorials/index" >}}Tutorials{{< /button >}}
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{{< button size="small" relref="usage/lexicmap" >}}Usages{{< /button >}}
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{{< button size="small" relref="faqs" >}}FAQs{{< /button >}}
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### Accurate and efficient alignment
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Using LexicMap to align in the whole **2,340,672** Genbank+Refseq prokaryotic genomes with 48 CPUs.
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Using LexicMap v0.7.0 to align against the whole **2,340,672** Genbank+Refseq prokaryotic genomes with 48 CPUs.
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|Query |Genome hits|Time |RAM(GB)|
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|:----------------|----------:|------:|------:|

‎docs/content/installation/_index.md‎

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|OS |Arch |File, 中国镜像 |
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|:------|:---------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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|Linux |**64-bit**|[**lexicmap_linux_amd64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.7.0/lexicmap_linux_amd64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_linux_amd64.tar.gz) |
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|Linux |arm64 |[**lexicmap_linux_arm64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.7.0/lexicmap_linux_arm64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_linux_arm64.tar.gz) |
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|Linux |**64-bit**|[**lexicmap_linux_amd64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.8.0/lexicmap_linux_amd64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_linux_amd64.tar.gz) |
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|Linux |arm64 |[**lexicmap_linux_arm64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.8.0/lexicmap_linux_arm64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_linux_arm64.tar.gz) |
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2. Decompress it:
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|OS |Arch |File, 中国镜像 |
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|:------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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|macOS |64-bit|[**lexicmap_darwin_amd64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.7.0/lexicmap_darwin_amd64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_darwin_amd64.tar.gz) |
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|macOS |**arm64** |[**lexicmap_darwin_arm64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.7.0/lexicmap_darwin_arm64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_darwin_arm64.tar.gz) |
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|macOS |64-bit |[**lexicmap_darwin_amd64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.8.0/lexicmap_darwin_amd64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_darwin_amd64.tar.gz) |
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|macOS |**arm64** |[**lexicmap_darwin_arm64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.8.0/lexicmap_darwin_arm64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_darwin_arm64.tar.gz) |
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2. Copy it to any directory in the environment variable `PATH`:
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|OS |Arch |File, 中国镜像 |
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|:------|:---------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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|FreeBSD|**64-bit**|[**lexicmap_freebsd_amd64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.7.0/lexicmap_freebsd_amd64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_freebsd_amd64.tar.gz) |
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|FreeBSD|**64-bit**|[**lexicmap_freebsd_amd64.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.8.0/lexicmap_freebsd_amd64.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_freebsd_amd64.tar.gz) |
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{{< /tab >}}
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|OS |Arch |File, 中国镜像 |
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|:------|:---------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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|Windows|**64-bit**|[**lexicmap_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.7.0/lexicmap_windows_amd64.exe.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_windows_amd64.exe.tar.gz)|
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|Windows|**64-bit**|[**lexicmap_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/LexicMap/releases/download/v0.8.0/lexicmap_windows_amd64.exe.tar.gz), [中国镜像](http://app.shenwei.me/data/lexicmap/lexicmap_windows_amd64.exe.tar.gz)|
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2. Decompress it.

‎docs/content/introduction/_index.md‎

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LexicMap is a **nucleotide sequence alignment** tool for efficiently querying **gene, plasmid, viral, or long-read sequences (>150 bp)** against up to **millions of prokaryotic genomes**.
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Source code: https://github.com/shenwei356/LexicMap
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For the latest features and improvements, please download the [pre-release binaries](https://github.com/shenwei356/LexicMap/issues/10).
1617

17-
Preprint:
18+
Please cite:
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1920
> Wei Shen, John A. Lees, Zamin Iqbal.
20-
> (2024) LexicMap: efficient sequence alignment against millions of prokaryotic genomes.
21-
> bioRxiv. [https://doi.org/10.1101/2024.08.30.610459](https://doi.org/10.1101/2024.08.30.610459)
22-
21+
> (2025) Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.
22+
> Nature Biotechnology. [https://doi.org/10.1038/s41587-025-02812-8](https://doi.org/10.1038/s41587-025-02812-8)
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## Table of contents
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- [Table of contents](#table-of-contents)
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- [Features](#features)
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- [Introduction](#introduction)
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- [Quick start](#quick-start)
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## Features
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1. **The accuracy of LexicMap is comparable with Blastn, MMseqs2, and Minimap2**. It
43-
- performs **base-level alignment**, with `qcovGnm`, `qcovHSP`, `pident`, `evalue` and `bitscore` returned,
42+
- **performs base-level alignment**, with `qcovGnm`, `qcovHSP`, `pident`, `evalue` and `bitscore` returned,
4443
both in TSV and pairwise alignment format ([output format](https://bioinf.shenwei.me/LexicMap/tutorials/search/#output)).
4544
- provides a genome-wide query coverage metric (`qcovGnm`),
4645
which enables accurate interpretation of search results - particularly for [circular queries (such as plasmid, virus, and mtDNA)](https://bioinf.shenwei.me/LexicMap/tutorials/search/#searching-with-plasmids-or-other-longer-queries)
4746
against both complete and fragmented assemblies.
48-
- returns all possible matches, including multiple copies of a gene in a genome.
47+
- **returns all possible matches**, including multiple copies of a gene in a genome.
4948
1. **The alignment is fast and memory-efficient, scalable to up to millions of prokaryotic genomes**.
5049
1. LexicMap is **easy to [install](http://bioinf.shenwei.me/LexicMap/installation/),
5150
we provide [binary files](https://github.com/shenwei356/LexicMap/releases/)** with no dependencies for Linux, Windows, MacOS (x86 and arm CPUs).
5251
2. LexicMap is **easy to use** (see [tutorials](http://bioinf.shenwei.me/LexicMap/tutorials/index/), [usages](http://bioinf.shenwei.me/LexicMap/usage/lexicmap/), and [FAQs](https://bioinf.shenwei.me/LexicMap/faqs/)).
5352
- [Database building](https://bioinf.shenwei.me/LexicMap/tutorials/index/) requires only a simple command, accepting input from files, a file list, or even a directory.
5453
- [Sequence searching](https://bioinf.shenwei.me/LexicMap/tutorials/search/) supports limiting search by TaxId(s), provides a progress bar.
55-
- [Several utility commands](https://bioinf.shenwei.me/LexicMap/usage/utils/) are available to resume unfinished indexing, and explore the index data, extract indexed subsequences.
54+
- [Several utility commands](https://bioinf.shenwei.me/LexicMap/usage/utils/) are available to resume unfinished indexing, explore the index data, merge search results, extract matched subsequences and more.
5655

5756
## Introduction
5857

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7978
1. LexicMap enables efficient indexing and searching of both RefSeq+GenBank and the [AllTheBacteria](https://www.biorxiv.org/content/10.1101/2024.03.08.584059v1) datasets (**2.3 and 1.9 million prokaryotic assemblies** respectively).
8079
1. When searching in all **2,340,672 Genbank+Refseq prokaryotic genomes**, *Blastn is unable to run with this dataset on common servers as it requires >2000 GB RAM*. (see [performance](#performance)).
8180

82-
**With LexicMap v0.7.0** (48 CPUs),
81+
**With LexicMap v0.7.0** (48 CPUs, indexes and queries queries in HDDs),
8382

8483
|Query |Genome hits|Genome hits<br/>(high-similarity)|Genome hits<br/>(medium-similarity)|Genome hits<br/>(low-similarity)|Time |RAM |
8584
|:-------------------|----------:|--------------------------------:|----------------------------------:|-------------------------------:|----------:|-------:|
@@ -93,8 +92,8 @@ However, given the increasing rate at which genomes are sequenced, **existing to
9392
1. Only the best alignment of a genome is used to evaluate alignment similarity:
9493
- high-similarity: (a) qcov >= 90% (genes) or 70% (plasmids), (b) pident>=90%.
9594
- medium-similarity: (a) not belong to high-similarity, (b) qcov >= 50% (genes) or 30% (plasmids), (c) pident>=80%.
96-
- low-similarity: left.
97-
1. The search time varies in different computing environments and mainly depends on the I/O speed.
95+
- low-similarity: the remaining.
96+
1. The search time varies in different computing environments and mainly depends on the I/O speed and the number of threads.
9897

9998
## Quick start
10099

@@ -238,8 +237,8 @@ See the [paper](#citation) for details.
238237
## Citation
239238

240239
> Wei Shen, John A. Lees, Zamin Iqbal.
241-
> (2024) LexicMap: efficient sequence alignment against millions of prokaryotic genomes.
242-
> bioRxiv. [https://doi.org/10.1101/2024.08.30.610459](https://doi.org/10.1101/2024.08.30.610459)
240+
> (2025) Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.
241+
> Nature Biotechnology. [https://doi.org/10.1038/s41587-025-02812-8](https://doi.org/10.1038/s41587-025-02812-8)
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## Limitations
245244

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