dada2 - Accurate, high-resolution sample inference from amplicon sequencing data
The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.
Last updated 24 days ago
immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioconductorbioinformaticsmetabarcodingtaxonomy
12.09 score 469 stars 4 packages 2.1k scripts 5.4k downloadsdecontam - Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples.
Last updated 24 days ago
immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioinformaticscontaminationmetabarcoding
11.35 score 147 stars 6 packages 454 scripts 2.3k downloads