Fast filtering, mapping and assembly of 16S ribosomal RNA

The application of next-generation sequencing technologies to RNA orDNA directly extracted from a community of organisms yields a mixtureof nucleotide fragments. The task to distinguish amongst these and tofurther categorize the families of ribosomal RNAs (or any other givenmarker) is an important step for examining the phylogeneticclassification of the constituting species. In thisperspective, we have developed a complete bioinformatics suite, called MATAM, capable of handling large sets of reads in a fast and accurate way. MATAM covers all steps of the analysis, from the identificationof reads of interest in the raw sequencing data to the reconstructionof the full-length sequences of the marker and alignment to areference database for taxonomic assignment. Part of MATAM is basedon the SortMeRNA software, also developed by the team.

Keywords: metagenomics

Licence: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0

Remote created date: 2016-12-16

Remote updated date: 2017-01-11

Fast filtering, mapping and assembly of 16S ribosomal RNA https://tess.elixir-europe.org/materials/fast-filtering-mapping-and-assembly-of-16s-ribosomal-rna-83398e0f-76de-4945-b0a8-8274413a6a47 The application of next-generation sequencing technologies to RNA orDNA directly extracted from a community of organisms yields a mixtureof nucleotide fragments. The task to distinguish amongst these and tofurther categorize the families of ribosomal RNAs (or any other givenmarker) is an important step for examining the phylogeneticclassification of the constituting species. In thisperspective, we have developed a complete bioinformatics suite, called MATAM, capable of handling large sets of reads in a fast and accurate way. MATAM covers all steps of the analysis, from the identificationof reads of interest in the raw sequencing data to the reconstructionof the full-length sequences of the marker and alignment to areference database for taxonomic assignment. Part of MATAM is basedon the SortMeRNA software, also developed by the team. metagenomics 2016-12-16 2017-01-11