Efficient inference of large prokaryotic pangenomes with PanTA
Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency l...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
BioMed Central
2024
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| _version_ | 1811140405165555712 |
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| author | Le, DQ Nguyen, TA Nguyen, SH Nguyen, TT Nguyen, CH Phung, HT Ho, TH Vo, NS Nguyen, T Nguyen, HA Cao, MD |
| author_facet | Le, DQ Nguyen, TA Nguyen, SH Nguyen, TT Nguyen, CH Phung, HT Ho, TH Vo, NS Nguyen, T Nguyen, HA Cao, MD |
| author_sort | Le, DQ |
| collection | OXFORD |
| description | Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces a novel mechanism to construct the pangenome progressively without rebuilding the accumulated collection from scratch. The progressive mode is shown to consume orders of magnitude less computational resources than existing solutions in managing growing datasets. The software is open source and is publicly available at https://github.com/amromics/panta and at 10.6084/m9.figshare.23724705. |
| first_indexed | 2024-09-25T04:21:27Z |
| format | Journal article |
| id | oxford-uuid:05a9e832-9ad3-4b34-8736-bd59762c49bb |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-09-25T04:21:27Z |
| publishDate | 2024 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:05a9e832-9ad3-4b34-8736-bd59762c49bb2024-08-15T20:03:44ZEfficient inference of large prokaryotic pangenomes with PanTAJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:05a9e832-9ad3-4b34-8736-bd59762c49bbEnglishJisc Publications RouterBioMed Central2024Le, DQNguyen, TANguyen, SHNguyen, TTNguyen, CHPhung, HTHo, THVo, NSNguyen, TNguyen, HACao, MDPangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces a novel mechanism to construct the pangenome progressively without rebuilding the accumulated collection from scratch. The progressive mode is shown to consume orders of magnitude less computational resources than existing solutions in managing growing datasets. The software is open source and is publicly available at https://github.com/amromics/panta and at 10.6084/m9.figshare.23724705. |
| spellingShingle | Le, DQ Nguyen, TA Nguyen, SH Nguyen, TT Nguyen, CH Phung, HT Ho, TH Vo, NS Nguyen, T Nguyen, HA Cao, MD Efficient inference of large prokaryotic pangenomes with PanTA |
| title | Efficient inference of large prokaryotic pangenomes with PanTA |
| title_full | Efficient inference of large prokaryotic pangenomes with PanTA |
| title_fullStr | Efficient inference of large prokaryotic pangenomes with PanTA |
| title_full_unstemmed | Efficient inference of large prokaryotic pangenomes with PanTA |
| title_short | Efficient inference of large prokaryotic pangenomes with PanTA |
| title_sort | efficient inference of large prokaryotic pangenomes with panta |
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