Libra
The "Libra" is for metagenomic analysis, leveraging a k–mer–based approach to facilitate massive all-vs-all metagenome comparisons. This tool stands out in its capacity to process and analyze large-scale metagenomic datasets, which is becoming increasingly crucial as the volume of genomic data generated by researchers grows exponentially.
Core Features and Functionality:
- Scalable k–mer–based Comparisons: Libra utilizes k-mers (subsequences of length k) to compare genetic sequences across different metagenomes. This approach is fundamental for capturing microbial communities' genetic diversity and composition without the need for reference genomes.
- All-vs-All Metagenome Comparison: It performs comprehensive comparisons, meaning every metagenome in a dataset is compared against every other, enabling deep and broad analysis of similarities and differences across microbial communities, particularly valuable for studies aimed at understanding microbial diversity, evolution, and the roles of microbes in different environments or host organisms.
- Scalability through Hadoop Framework: One of the most significant challenges in metagenomic analysis is the computational demand of processing vast amounts of data. Libra addresses this challenge by employing a scalable Hadoop framework, which allows it to efficiently manage and analyze large datasets by distributing the computing load across multiple nodes in a cluster.
- Cosine Similarity for Distance Calculation: Libra uses Cosine Similarity measures to calculate the distance between metagenomes based on their k-mer content. This metric considers both the presence and abundance of k-mers, while also normalizing for sequencing depth, which ensures that the comparisons are accurate and reflective of the true biological differences between samples.
- Web-based Implementation and Accessibility: Libra is implemented as a web-based tool, hosted on platforms like iMicrobe, and benefits from the CyVerse advanced cyberinfrastructure. This web-based approach enhances its accessibility, allowing researchers from around the globe to utilize the tool without the need to install complex software or manage large computational resources locally.
Topic
Metagenomics;Metagenomic sequencing;Biodiversity
Detail
Operation: k-mer counting;Expression analysis;Sequence assembly
Software interface: Command-line interface, web user interface
Language: Java
License: Apache License, Version 2.0
Cost: Free with restrictions
Version name: -
Credit: National Science Foundation, University of Arizona Information Technology Services, BEI Resources, National Institute of Allergy and Infectious diseases (NIAID), National Institutes of Health (NIH).
Input: -
Output: -
Contact: Illyoung Choi iychoi@email.arizona.edu
Collection: -
Maturity: Mature
Publications
- A guided tour of the Trans-Proteomic Pipeline.
- Deutsch EW, et al. A guided tour of the Trans-Proteomic Pipeline. A guided tour of the Trans-Proteomic Pipeline. 2010; 10:1150-9. doi: 10.1002/pmic.200900375
- https://doi.org/10.1002/pmic.200900375
- PMID: 20101611
- PMC: PMC3017125
- Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.
- Choi I, et al. Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons. Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons. 2019; 8:(unknown pages). doi: 10.1093/gigascience/giy165
- https://doi.org/10.1093/gigascience/giy165
- PMID: 30597002
- PMC: PMC6354030
Download and documentation
Source: https://github.com/iychoi/libra/releases/download/v1.2.5/libra-all.jar
Documentation: https://github.com/iychoi/libra/blob/master/README.md
Home page: https://github.com/iychoi/libra
Links: https://www.imicrobe.us/
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