Removal of sequencing adapter contamination improves microbial genome databases
Abstract Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-11-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-10956-1 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850196486066798592 |
|---|---|
| author | Andrew H. Moeller Brian A. Dillard Samantha L. Goldman Madalena V. F. Real Daniel D. Sprockett |
| author_facet | Andrew H. Moeller Brian A. Dillard Samantha L. Goldman Madalena V. F. Real Daniel D. Sprockett |
| author_sort | Andrew H. Moeller |
| collection | DOAJ |
| description | Abstract Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases. |
| format | Article |
| id | doaj-art-bb791503e7804d289d2e3202cacd083c |
| institution | OA Journals |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-bb791503e7804d289d2e3202cacd083c2025-08-20T02:13:27ZengBMCBMC Genomics1471-21642024-11-012511610.1186/s12864-024-10956-1Removal of sequencing adapter contamination improves microbial genome databasesAndrew H. Moeller0Brian A. Dillard1Samantha L. Goldman2Madalena V. F. Real3Daniel D. Sprockett4Department of Ecology and Evolutionary Biology, Princeton UniversityDepartment of Ecology and Evolutionary Biology, Cornell UniversityDepartment of Ecology and Evolutionary Biology, Cornell UniversityDepartment of Ecology and Evolutionary Biology, Cornell UniversityDepartment of Ecology and Evolutionary Biology, Cornell UniversityAbstract Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.https://doi.org/10.1186/s12864-024-10956-1Bacterial genomesMetagenomeMicrobiotaSymbiosisMicrobial ecology |
| spellingShingle | Andrew H. Moeller Brian A. Dillard Samantha L. Goldman Madalena V. F. Real Daniel D. Sprockett Removal of sequencing adapter contamination improves microbial genome databases BMC Genomics Bacterial genomes Metagenome Microbiota Symbiosis Microbial ecology |
| title | Removal of sequencing adapter contamination improves microbial genome databases |
| title_full | Removal of sequencing adapter contamination improves microbial genome databases |
| title_fullStr | Removal of sequencing adapter contamination improves microbial genome databases |
| title_full_unstemmed | Removal of sequencing adapter contamination improves microbial genome databases |
| title_short | Removal of sequencing adapter contamination improves microbial genome databases |
| title_sort | removal of sequencing adapter contamination improves microbial genome databases |
| topic | Bacterial genomes Metagenome Microbiota Symbiosis Microbial ecology |
| url | https://doi.org/10.1186/s12864-024-10956-1 |
| work_keys_str_mv | AT andrewhmoeller removalofsequencingadaptercontaminationimprovesmicrobialgenomedatabases AT brianadillard removalofsequencingadaptercontaminationimprovesmicrobialgenomedatabases AT samanthalgoldman removalofsequencingadaptercontaminationimprovesmicrobialgenomedatabases AT madalenavfreal removalofsequencingadaptercontaminationimprovesmicrobialgenomedatabases AT danieldsprockett removalofsequencingadaptercontaminationimprovesmicrobialgenomedatabases |