plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets [version 2; peer review: 1 approved, 2 approved with reservations]
The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic c...
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Wellcome
2024-11-01
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| Online Access: | https://wellcomeopenresearch.org/articles/8-475/v2 |
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| author | Robert D. Finn Ellen S. Cameron Mark L. Blaxter |
| author_facet | Robert D. Finn Ellen S. Cameron Mark L. Blaxter |
| author_sort | Robert D. Finn |
| collection | DOAJ |
| description | The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes. |
| format | Article |
| id | doaj-art-d3af8c07c9f34bc4bc06ba4e0e665abe |
| institution | DOAJ |
| issn | 2398-502X |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Wellcome |
| record_format | Article |
| series | Wellcome Open Research |
| spelling | doaj-art-d3af8c07c9f34bc4bc06ba4e0e665abe2025-08-20T02:56:33ZengWellcomeWellcome Open Research2398-502X2024-11-01810.12688/wellcomeopenres.19589.225383plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets [version 2; peer review: 1 approved, 2 approved with reservations]Robert D. Finn0Ellen S. Cameron1https://orcid.org/0000-0003-3931-4245Mark L. Blaxter2https://orcid.org/0000-0001-5902-6641EMBL-EBI European Bioinformatics Institute, Hinxton, CB10 1SD, UKEMBL-EBI European Bioinformatics Institute, Hinxton, CB10 1SD, UKTree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UKThe use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes.https://wellcomeopenresearch.org/articles/8-475/v2chloroplasts metagenomics chloroplast genome Snakemake workflow metagenomic assembled genomeseng |
| spellingShingle | Robert D. Finn Ellen S. Cameron Mark L. Blaxter plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets [version 2; peer review: 1 approved, 2 approved with reservations] Wellcome Open Research chloroplasts metagenomics chloroplast genome Snakemake workflow metagenomic assembled genomes eng |
| title | plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_full | plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_fullStr | plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_full_unstemmed | plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_short | plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_sort | plastic a pipeline for recovery and characterization of plastid genomes from metagenomic datasets version 2 peer review 1 approved 2 approved with reservations |
| topic | chloroplasts metagenomics chloroplast genome Snakemake workflow metagenomic assembled genomes eng |
| url | https://wellcomeopenresearch.org/articles/8-475/v2 |
| work_keys_str_mv | AT robertdfinn plasticapipelineforrecoveryandcharacterizationofplastidgenomesfrommetagenomicdatasetsversion2peerreview1approved2approvedwithreservations AT ellenscameron plasticapipelineforrecoveryandcharacterizationofplastidgenomesfrommetagenomicdatasetsversion2peerreview1approved2approvedwithreservations AT marklblaxter plasticapipelineforrecoveryandcharacterizationofplastidgenomesfrommetagenomicdatasetsversion2peerreview1approved2approvedwithreservations |