RT Conference Proceedings
T1 Analyzing the differences between reads and contigs when performing a taxonomic assignment comparison in metagenomics
A1 Rodríguez-Brazzarola, Pablo
A1 Perez-Wohlfeil, Esteban
A1 Díaz-del-Pino, Sergio
A1 Holthausen, Ricardo
A1 Trelles-Salazar, Oswaldo Rogelio
K1 Bioinformática - Congresos
AB Metagenomics is an inherently complex field in which one ofthe primary goals is to determine the compositional organisms presentin an environmental sample. Thereby, diverse tools have been developedthat are based on the similarity search results obtained from comparinga set of sequences against a database. However, to achieve this goalthere still are affairs to solve such as dealing with genomic variants anddetecting repeated sequences that could belong to different species in amixture of uneven and unknown representation of organisms in a sample.Hence, the question of whether analyzing a sample with reads providesfurther understanding of the metagenome than with contigs arises. Theassembly yields larger genomic fragments but bears the risk of producingchimeric contigs. On the other hand, reads are shorter and thereforetheir statistical significance is harder to asses, but there is a larger numberof them. Consequently, we have developed a workflow to assess andcompare the quality of each of these alternatives. Synthetic read datasetsbeloging to previously identified organisms are generated in order to validatethe results. Afterwards, we assemble these into a set of contigs andperform a taxonomic analysis on both datasets. The tools we have developeddemonstrate that analyzing with reads provide a more trustworthyrepresentation of the species in a sample than contigs especially in casesthat present a high genomic variability.
PB Springer, Cham
YR 2018
FD 2018-03
LK https://hdl.handle.net/10630/15737
UL https://hdl.handle.net/10630/15737
LA eng
NO Rodríguez-Brazzarola P., Pérez-Wohlfeil E., Díaz-del-Pino S., Holthausen R., Trelles O. (2018) Analyzing the Differences Between Reads and Contigs When Performing a Taxonomic Assignment Comparison in Metagenomics. In: Rojas I., Ortuño F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2018. Lecture Notes in Computer Science, vol 10813. Springer, Cham
NO Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech.
DS RIUMA. Repositorio Institucional de la Universidad de Málaga
RD 20 ene 2026