Genomic Distance-based Rapid Uncovering of Microbial Population Structures (GRUMPS): a reference free genomic data cleaning methodology
Abram, K. Z.; Udaondo, Z.; Nookaew, I.; Robeson, M. S.; Jun, S.-R.
Show abstract
Accurate datasets are crucial for rigorous large-scale sequence-based analyses such as those performed in phylogenomics and pangenomics. As the volume of available sequence data grows and the quality of these sequences varies, there is a pressing need for reliable methods to swiftly identify and eliminate low-quality and misidentified genomes from datasets prior to analysis. Here we introduce a robust, controlled, computationally efficient method for deriving species-level population structures of bacterial species, regardless of the dataset size. Additionally, our pipeline can classify genomes into their respective species at the genus level. By leveraging this methodology, researchers can rapidly clean datasets encompassing entire bacterial species and examine the sub-species population structures within the provided genomes. These cleaned datasets can subsequently undergo further refinement using a variety of methods to yield sequence sets with varying levels of diversity that faithfully represent entire species. Increasing the efficiency and accuracy of curation of species-level datasets not only enhances the reliability of downstream analyses, but also facilitates a deeper understanding of bacterial population dynamics and evolution.
Matching journals
The top 8 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- cognac: rapid generation of concatenated gene alignments for phylogenetic inferencefrom large whole genome sequencing datasets 97%
- PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes 96%
- Functional Analysis of Metagenomes by Likelihood Inference (FAMLI) Successfully Compensates for Multi-Mapping Short Reads from Metagenomic Samples 95%
Similar papers in this journal
- Life at the extremes: Maximally divergent microbes with similar genomic signatures linked to extreme environments 96%
- Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine Learning-Enabled Resource Allocation 96%
- ganon2: up-to-date and scalable metagenomics analysis 95%
Similar papers in this journal
- Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure 96%
- From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools 95%
- Bakta: Rapid & standardized annotation of bacterial genomes via alignment-free sequence identification 95%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.