Ciuffreda, L. | Search bioRxiv

bioRxiv2020

NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data

SummaryNanoCLUST is an analysis pipeline for classification of amplicon-based full-length 16S rRNA nanopore reads. It is characterized by an unsupervised read clustering step, based on Uniform Manifold Approximation and Projection (UMAP), followed by the construction of a polished read and subsequent Blast classification. Here we demonstrate that NanoCLUST performs better than other state-of-the-art software in the characterization of two commercial mock communities, enabling accurate bacterial identification and abundance profile estimation at species level resolution. Availability and implementationSource code, test data and documentation of NanoCLUST is freely available at https://github.com/genomicsITER/NanoCLUST under MIT License. Contactcflores@ull.edu.es

bioinformatics↗

bioRxiv2017

Detection Of Human Disease Conditions By Single-Cell Morpho-Rheological Phenotyping Of Whole Blood

Blood is arguably the most important bodily fluid and its analysis provides crucial health status information. A first routine measure to narrow down diagnosis in clinical practice is the differential blood count, determining the frequency of all major blood cells. What is lacking to advance initial blood diagnostics is an unbiased and quick functional assessment of blood that can narrow down the diagnosis and generate specific hypotheses. To address this need, we introduce the continuous, cell-by-cell morpho-rheological (MORE) analysis of whole blood, without labeling, enrichment or separation, at rates of 1,000 cells/sec. In a drop of blood we can identify all major blood cells and characterize their pathological changes in several disease conditions in vitro and in patient samples. This approach takes previous results of mechanical studies on specifically isolated blood cells to the level of application directly in whole blood and adds a functional dimension to conventional blood analysis.

biophysics↗