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Use when working with OBITools3 for DNA metabarcoding, environmental DNA, primer/tag demultiplexing, paired-end read assembly, dereplication, denoising, taxonomic assignment, or export from the OBIToo
Use with AI
Install the MCP server or CLI to instantly fetch OBITools3 documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/obitools3
GATK4 — Genome Analysis Toolkit for germline and somatic short variant discovery (SNPs and indels). Industry-standard caller providing HaplotypeCaller for germline, Mutect2 for somatic, plus Base Qual
1 shared topic • 2 shared operations
Meryl — fast k-mer counting and set-operation toolkit from the Marbl group (Canu/Verkko). Counts canonical or strand-specific k-mers from FASTA/FASTQ inputs into binary meryl databases, then supports
1 shared topic • 2 shared operations
Mutect2 -- GATK somatic short variant caller for detecting SNVs and indels in tumor samples. Supports tumor-only and tumor-normal paired calling modes with Panel of Normals and germline resource filte
1 shared topic • 2 shared operations
ncbi-genome-download is a Python CLI tool and library for bulk downloading genome sequences and associated files from NCBI RefSeq and GenBank FTP servers. Supports all taxonomic groups (bacteria, fung
1 shared topic • 2 shared operations
Pharokka — fast, scalable bacteriophage genome annotation. Annotates phage genomes using pyhmmer (PHROGs), MMseqs2 (CARD, VFDB, COG), and tRNAscan-SE. Produces GenBank, GFF3, and tabular outputs in mi
1 shared topic • 2 shared operations