The taxonomic analysis of sequencing data has become important in many areas of life sciences. However, currently available tools for that purpose either consume large amounts of RAM or yield insufficient quality and robustness. Here, we present kASA, a k-mer based tool capable of identifying and profiling metagenomic DNA or protein sequences with high computational efficiency and a user-definable memory footprint. We ensure both high sensitivity and precision by using an amino acid-like encoding of k-mers together with a range of multiple k's. Custom algorithms and data structures optimized for external memory storage enable a full-scale taxonomic analysis without compromise on laptop, desktop, and HPCC.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8266618 | PMC |
| http://dx.doi.org/10.1093/nar/gkab200 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Clinical and laboratory characteristics of Sjögren's syndrome-associated autoimmune liver disease: a real-world, 10-year retrospective study.
Clin Rheumatol
January 2025
Department of Rheumatology and Immunology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China.
Objectives: To investigate the clinical and laboratory features of Sjögren's syndrome-associated autoimmune liver disease (SS-ALD) patients and identify potential risk and prognostic factors.
Methods: SS patients with or without ALD, who visited Tongji Hospital between the years 2011 and 2021 and met the 2012 American College of Rheumatology (ACR) classification criteria for Sjögren's syndrome, were retrospectively enrolled. The clinical and laboratory data of the enrolled patients, including autoimmune antibodies, were collected and analyzed with principal component analysis, correlation analysis, LASSO regression, and Cox regression.
Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications.
World J Microbiol Biotechnol
January 2025
Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
Mammalian milk contains a variety of complex bioactive and nutritional components and microorganisms. These microorganisms have diverse compositions and functional roles that impact host health and disease pathophysiology, especially mastitis. The advent and use of high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well as culturomics in milk microbiome studies suggest strong relationships between host phenotype and milk microbiome signatures in mastitis.
View Article and Find Full Text PDFRange-wide understanding of genetic diversity and population structure of endangered Kashmir musk deer in North-Western Himalaya.
Mol Biol Rep
January 2025
Zoological Survey of India, Kolkata, 700053, India.
Background: The endangered Kashmir musk deer (Moschus cupreus), native to high-altitude Himalayas, is an ecological significant and endangered ungulate, threatened by habitat loss and poaching for musk pod distributed in western Himalayan ranges of India, Nepal and Afghanistan. Despite its critical conservation status and ecological importance in regulating vegetation dynamics, knowledge gaps persist regarding its population structure and genetic diversity, hindering effective management strategies.
Methods And Results: We aimed to understand the population genetics of Kashmir musk deer in north-western Himalayas using two mitochondrial DNA (mtDNA) regions and 11 microsatellite loci.
Cerebrovascular risk in rheumatoid arthritis patients: insights from carotid artery atherosclerosis in the Paracelsus 10,000 study.
Rheumatol Int
January 2025
Department of Internal Medicine, General Hospital Oberndorf, Teaching Hospital of the Paracelsus Medical University, Salzburg, Austria.
Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by systemic inflammation. While RA primarily affects the joints, its systemic effects may lead to an increased cerebro- and cardiovascular risk. Atherosclerosis of the carotid arteries is a significant risk factor for cerebrovascular events and serves as a surrogate marker for cardiovascular risk.
View Article and Find Full Text PDFEnhanced Mosquito Larvicidal Efficacy and Dehairing Properties of Bacillus thuringiensis Serovar israelensis Strain VCRC-B649 Isolated from Malabar Coast, India.
Curr Microbiol
January 2025
Unit of Microbiology and Immunology, ICMR-Vector Control Research Centre, Medical Complex, Indira Nagar, Puducherry, 605006, India.
In recent years, there has been a global threat from emerging vector-borne diseases (VBD), despite the implementation of several vector control programs. Considering the benefits of bacterial pesticides, the present study aimed to isolate potential mosquitocidal bacteria from the various soil types collected from the Kasaragod (12.5°N, 75.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!