happi: a hierarchical approach to pangenomics inference
Abstract Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms. However, metagenome-assembled genomes vary in...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-023-03040-6 |
| _version_ | 1797559404169527296 |
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| author | Pauline Trinh David S. Clausen Amy D. Willis |
| author_facet | Pauline Trinh David S. Clausen Amy D. Willis |
| author_sort | Pauline Trinh |
| collection | DOAJ |
| description | Abstract Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms. However, metagenome-assembled genomes vary in quality and may contain omissions and contamination. These errors present challenges for detecting genes and comparing gene enrichment across sample types. To address this, we propose happi, an approach to testing hypotheses about gene enrichment that accounts for genome quality. We illustrate the advantages of happi over existing approaches using published Saccharibacteria MAGs, Streptococcus thermophilus MAGs, and via simulation. |
| first_indexed | 2024-03-10T17:44:53Z |
| format | Article |
| id | doaj.art-6f73b8bc342d44ea829ff6fba2400e07 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-10T17:44:53Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-6f73b8bc342d44ea829ff6fba2400e072023-11-20T09:35:12ZengBMCGenome Biology1474-760X2023-09-0124111510.1186/s13059-023-03040-6happi: a hierarchical approach to pangenomics inferencePauline Trinh0David S. Clausen1Amy D. Willis2Department of Environmental & Occupational Health Sciences, University of WashingtonDepartment of Biostatistics, University of WashingtonDepartment of Biostatistics, University of WashingtonAbstract Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms. However, metagenome-assembled genomes vary in quality and may contain omissions and contamination. These errors present challenges for detecting genes and comparing gene enrichment across sample types. To address this, we propose happi, an approach to testing hypotheses about gene enrichment that accounts for genome quality. We illustrate the advantages of happi over existing approaches using published Saccharibacteria MAGs, Streptococcus thermophilus MAGs, and via simulation.https://doi.org/10.1186/s13059-023-03040-6Shotgun metagenomicsMetagenome-assembled genomesMicrobiomeStatistical modelsHypothesis testing |
| spellingShingle | Pauline Trinh David S. Clausen Amy D. Willis happi: a hierarchical approach to pangenomics inference Genome Biology Shotgun metagenomics Metagenome-assembled genomes Microbiome Statistical models Hypothesis testing |
| title | happi: a hierarchical approach to pangenomics inference |
| title_full | happi: a hierarchical approach to pangenomics inference |
| title_fullStr | happi: a hierarchical approach to pangenomics inference |
| title_full_unstemmed | happi: a hierarchical approach to pangenomics inference |
| title_short | happi: a hierarchical approach to pangenomics inference |
| title_sort | happi a hierarchical approach to pangenomics inference |
| topic | Shotgun metagenomics Metagenome-assembled genomes Microbiome Statistical models Hypothesis testing |
| url | https://doi.org/10.1186/s13059-023-03040-6 |
| work_keys_str_mv | AT paulinetrinh happiahierarchicalapproachtopangenomicsinference AT davidsclausen happiahierarchicalapproachtopangenomicsinference AT amydwillis happiahierarchicalapproachtopangenomicsinference |