FoodMicrobionet

NetCoMi (Network Construction and Comparison for Microbiome Data) — R package for constructing, analyzing, and comparing microbial association and dissimilarity networks from compositional count data.

3 shared topics

DADA2 — high-resolution amplicon sequence variant (ASV) inference from Illumina, 454, and Ion Torrent amplicon sequencing data. R/Bioconductor package that models sequencing errors to resolve exact bi

2 shared topics • 1 shared operation

LotuS2 (Less OTU Scripts 2) — ultrafast amplicon sequencing pipeline for 16S, 18S, 23S, 28S, and ITS marker gene analysis of microbial communities. Processes raw FASTQ/FASTA through demultiplexing (sd

2 shared topics • 1 shared operation

Pavian — interactive R/Shiny web application for metagenomics analysis and visualization. Reads classification reports from Kraken, Kraken2, Bracken, MetaPhlAn, DIAMOND+MEGAN, and Centrifuge to genera

2 shared topics • 1 shared operation

VSEARCH — open-source, multithreaded alternative to USEARCH for amplicon and metagenomics sequence analysis. Performs dereplication, chimera detection (de novo and reference-based), OTU/ASV clustering

2 shared topics • 1 shared operation