RESUMO
Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME. Availability and implementation: Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr. Contact: geraldine.pascal@inra.fr. Supplementary information: Supplementary data are available at Bioinformatics online.
Assuntos
Metagenômica/métodos , Software , Bactérias/genética , Análise por ConglomeradosRESUMO
O carcinoma adenoescamoso primário do estômago é um tumor raro, cuja incidência não excede 1 por cento dos tumores gástricos. Esse tumor mostra dois tipos celulares distintos: um escamoso e outro adenocarcinomatoso. É discutido um caso de um tumor raro e interessante do estômago, com relação à sua patogênese, diagnóstico e aspectos clínico-patológicos. Material e método: Reporta-se um caso de carcinoma adenoescamoso primário do estômago em uma paciente de cor branca de 51 anos, cuja patologia, exame endoscópico e histopatológico mostram a presença dos dois tipos celulares: adenocarcinomatoso e escamoso