bamAlignCleaner

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

1 shared topic • 2 shared operations

SILVA — comprehensive quality-checked database of aligned ribosomal RNA (rRNA) sequences for Bacteria, Archaea, and Eukaryota. Provides SSU (16S/18S) and LSU (23S/28S) rRNA reference databases for tax

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

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

Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short

1 shared topic • 1 shared operation