QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq

• Autores: Bruno Cavadas, Joana Ferreira, Rui Camacho, Nuno A. Fonseca, Luisa Pereira
• Localización: 11th International Conference on Practical Applications of Computational Biology & Bioinformatics / Florentino Fernández Riverola (ed. lit.), 2017, ISBN 978-3-319-60815-0, págs. 173-179
• Idioma: inglés
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• Resumen

  • The huge amount of genomic and transcriptomic data obtained to characterize human diversity can also be exploited to indirectly gather informa‐ tion on the human microbiome. Here we present the pipeline QmihR designed to identify and quantify the abundance of known microbiome communities and to search for new/rare pathogenic species in RNA-seq datasets. We applied QmihR to 36 RNA-seq tumor tissue samples from Ukrainian gastric carcinoma patients available in TCGA, in order to characterize their microbiome and check for effi‐ ciency of the pipeline. The microbes present in the samples were in accordance to published data in other European datasets, and the independent BLAST eval‐ uation of microbiome-aligned reads confirmed that the assigned species presented the highest BLAST match-hits. QmihR is available at GitHub (https://github.com/ Pereira-lab/QmihR).