USEARCH

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

1 shared topic • 2 shared operations

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

1 shared topic • 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

1 shared topic • 2 shared operations

bamAlignCleaner — removes unaligned references from BAM/CRAM alignment files. Cleans alignment files by filtering out reference sequences with no mapped reads, reducing file size and speeding downstre

1 shared topic • 1 shared operation

BBDuk (Decontamination Using Kmers) — high-performance Java tool from the BBTools suite for adapter trimming, quality trimming, contaminant filtering, sequence masking, GC filtering, and format conver

1 shared topic • 1 shared operation