SILVA

Use when working with the ARTIC viral amplicon sequencing command-line pipeline for Oxford Nanopore data. Covers documented `artic minion`, `artic guppyplex`, and `artic_get_models` workflows for prim

2 shared topics • 2 shared operations

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 • 2 shared operations

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

EMU (Exact Mapping-based Unambiguous) — species-level 16S rRNA taxonomic profiling for long-read sequencing data (Oxford Nanopore, PacBio). Uses an expectation-maximization algorithm to resolve multi-

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