Cargando…
LMAS: evaluating metagenomic short de novo assembly methods through defined communities
BACKGROUND: The de novo assembly of raw sequence data is key in metagenomic analysis. It allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences that offer contextual information and provide a more complete picture of the microbial community. FINDINGS: To better com...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9795473/ https://www.ncbi.nlm.nih.gov/pubmed/36576131 http://dx.doi.org/10.1093/gigascience/giac122 |
_version_ | 1784860269407633408 |
---|---|
author | Mendes, Catarina Inês Vila-Cerqueira, Pedro Motro, Yair Moran-Gilad, Jacob Carriço, João André Ramirez, Mário |
author_facet | Mendes, Catarina Inês Vila-Cerqueira, Pedro Motro, Yair Moran-Gilad, Jacob Carriço, João André Ramirez, Mário |
author_sort | Mendes, Catarina Inês |
collection | PubMed |
description | BACKGROUND: The de novo assembly of raw sequence data is key in metagenomic analysis. It allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences that offer contextual information and provide a more complete picture of the microbial community. FINDINGS: To better compare de novo assemblers for metagenomic analysis, LMAS (Last Metagenomic Assembler Standing) was developed as a flexible platform allowing users to evaluate assembler performance given known standard communities. Overall, in our test datasets, k-mer De Bruijn graph assemblers outperformed the alternative approaches but came with a greater computational cost. Furthermore, assemblers branded as metagenomic specific did not consistently outperform other genomic assemblers in metagenomic samples. Some assemblers still in use, such as ABySS, MetaHipmer2, minia, and VelvetOptimiser, perform relatively poorly and should be used with caution when assembling complex samples. Meaningful strain resolution at the single-nucleotide polymorphism level was not achieved, even by the best assemblers tested. CONCLUSIONS: The choice of a de novo assembler depends on the computational resources available, the replicon of interest, and the major goals of the analysis. No single assembler appeared an ideal choice for short-read metagenomic prokaryote replicon assembly, each showing specific strengths. The choice of metagenomic assembler should be guided by user requirements and characteristics of the sample of interest, and LMAS provides an interactive evaluation platform for this purpose. LMAS is open source, and the workflow and its documentation are available at https://github.com/B-UMMI/LMAS and https://lmas.readthedocs.io/, respectively. |
format | Online Article Text |
id | pubmed-9795473 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-97954732022-12-28 LMAS: evaluating metagenomic short de novo assembly methods through defined communities Mendes, Catarina Inês Vila-Cerqueira, Pedro Motro, Yair Moran-Gilad, Jacob Carriço, João André Ramirez, Mário Gigascience Technical Note BACKGROUND: The de novo assembly of raw sequence data is key in metagenomic analysis. It allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences that offer contextual information and provide a more complete picture of the microbial community. FINDINGS: To better compare de novo assemblers for metagenomic analysis, LMAS (Last Metagenomic Assembler Standing) was developed as a flexible platform allowing users to evaluate assembler performance given known standard communities. Overall, in our test datasets, k-mer De Bruijn graph assemblers outperformed the alternative approaches but came with a greater computational cost. Furthermore, assemblers branded as metagenomic specific did not consistently outperform other genomic assemblers in metagenomic samples. Some assemblers still in use, such as ABySS, MetaHipmer2, minia, and VelvetOptimiser, perform relatively poorly and should be used with caution when assembling complex samples. Meaningful strain resolution at the single-nucleotide polymorphism level was not achieved, even by the best assemblers tested. CONCLUSIONS: The choice of a de novo assembler depends on the computational resources available, the replicon of interest, and the major goals of the analysis. No single assembler appeared an ideal choice for short-read metagenomic prokaryote replicon assembly, each showing specific strengths. The choice of metagenomic assembler should be guided by user requirements and characteristics of the sample of interest, and LMAS provides an interactive evaluation platform for this purpose. LMAS is open source, and the workflow and its documentation are available at https://github.com/B-UMMI/LMAS and https://lmas.readthedocs.io/, respectively. Oxford University Press 2022-12-28 /pmc/articles/PMC9795473/ /pubmed/36576131 http://dx.doi.org/10.1093/gigascience/giac122 Text en © The Author(s) 2022. Published by Oxford University Press GigaScience. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Technical Note Mendes, Catarina Inês Vila-Cerqueira, Pedro Motro, Yair Moran-Gilad, Jacob Carriço, João André Ramirez, Mário LMAS: evaluating metagenomic short de novo assembly methods through defined communities |
title | LMAS: evaluating metagenomic short de novo assembly methods through defined communities |
title_full | LMAS: evaluating metagenomic short de novo assembly methods through defined communities |
title_fullStr | LMAS: evaluating metagenomic short de novo assembly methods through defined communities |
title_full_unstemmed | LMAS: evaluating metagenomic short de novo assembly methods through defined communities |
title_short | LMAS: evaluating metagenomic short de novo assembly methods through defined communities |
title_sort | lmas: evaluating metagenomic short de novo assembly methods through defined communities |
topic | Technical Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9795473/ https://www.ncbi.nlm.nih.gov/pubmed/36576131 http://dx.doi.org/10.1093/gigascience/giac122 |
work_keys_str_mv | AT mendescatarinaines lmasevaluatingmetagenomicshortdenovoassemblymethodsthroughdefinedcommunities AT vilacerqueirapedro lmasevaluatingmetagenomicshortdenovoassemblymethodsthroughdefinedcommunities AT motroyair lmasevaluatingmetagenomicshortdenovoassemblymethodsthroughdefinedcommunities AT morangiladjacob lmasevaluatingmetagenomicshortdenovoassemblymethodsthroughdefinedcommunities AT carricojoaoandre lmasevaluatingmetagenomicshortdenovoassemblymethodsthroughdefinedcommunities AT ramirezmario lmasevaluatingmetagenomicshortdenovoassemblymethodsthroughdefinedcommunities |