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strollur - Store and Transfer Amplicon Sequence Data

Stores the data associated with your amplicon sequence analysis. This includes nucleotide sequences, abundance, sample and treatment assignments, taxonomic classifications, asv, otu and phylotype clusters, metadata, trees and various reports. It is designed to facilitate data analysis across multiple R packages with utility functions to read / write from 'mothur', 'qiime2', 'dada2', and 'phyloseq'.

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amplicon-sequencingasvotusphylogenetic-analysiscpp

6.51 score 1 dependents 10 scripts 440 downloads

phylotypr - Classifying DNA Sequences to Taxonomic Groupings

Classification based analysis of DNA sequences to taxonomic groupings. This package primarily implements Naive Bayesian Classifier from the Ribosomal Database Project. This approach has traditionally been used to classify 16S rRNA gene sequences to bacterial taxonomic outlines; however, it can be used for any type of gene sequence. The method was originally described by Wang, Garrity, Tiedje, and Cole in Applied and Environmental Microbiology 73(16):5261-7 <doi:10.1128/AEM.00062-07>. The package also provides functions to read in 'FASTA'-formatted sequence data.

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cpp

5.88 score 10 stars 8 scripts 270 downloads

rchime - Detect and Remove Chimeras from Amplicon Sequence Analysis Data

Detect and remove chimeras from your amplicon sequence analysis using reference-based or de novo approaches. The 'rchime' package implements the 'VSEARCH' algorithms described in Rognes et al. (2016) <doi:10.7717/peerj.2584>. 'VSEARCH' builds on the work of Edgar,R.C. et al. (2011) <doi:10.1093/bioinformatics/btr381>.

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amplicon-sequencingchimeracpp

5.51 score 5 scripts 264 downloads