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M-CAMP™: A cloud-based web platform with a novel approach for species-level classification of 16S rRNA microbiome sequences

Schriefer, A. E.; Kumar, B.; Zolty, A.; R, P.; Didier, A.; MG, N.; Nadiv, N.; Perez, M.; Mahankuda, S. K.; Kumar, P.; GT, G.; Tenney, A.; Bourner, M.; Lezer, S.; Zhong, F.; Daniely, M.; Liu, Y.

2021-08-27 bioinformatics
10.1101/2021.08.25.456838 bioRxiv
Show abstract

The M-CAMP (Microbiome Computational Analysis for Multiomic Profiling) Cloud Platform was designed to provide users with an easy-to-use web interface to access best in class microbiome analysis tools. This interface allows bench scientists to conduct bioinformatic analysis on their samples and then download publication-ready graphics and reports. The core pipeline of the platform is the 16S-seq taxonomic classification algorithm which provides species-level classification of Illumina 16s sequencing. This algorithm uses a novel approach combining alignment and kmer based taxonomic classification methodologies to produce a highly accurate and comprehensive profile. Additionally, a comprehensive proprietary database combining reference sequences from multiple sources was curated and contains 18056 unique V3-V4 sequences covering 11527 species. The M-CAMP 16S taxonomic classification algorithm was validated on 52 sequencing samples from both public and in-house standard sample mixtures with known fractions. Compared to current popular public classification algorithms, our classification algorithm provides the most accurate species-level classification of 16S rRNA sequencing data.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.