DADA2

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

Use when working with iVar for viral amplicon sequencing, primer trimming, intrahost variant calling, consensus generation, replicate-aware variant filtering, or primer mismatch masking workflows. iVa

2 shared topics • 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

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

VarDict variant caller for SNVs, MNVs, indels, complex variants, and structural variants from BAM files. Supports somatic paired tumor-normal calling and single-sample germline mode. Ultra-sensitive v

2 shared topics • 1 shared operation