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Use when working with CutITS, the command-line tool for extracting and trimming ITS (Internal Transcribed Spacer) regions from fungal amplicon sequencing reads. Covers ITS1, ITS2, and full ITS extract
Use with AI
Install the MCP server or CLI to instantly fetch CutITS documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/cutits
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
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