blastn-vdb

name	blastn-vdb
description	Use when searching nucleotide sequences against SRA/VDB databases using BLAST. Invokes blastn_vdb for nucleotide-nucleotide alignment with SRA accessions.
disable-model-invocation	true
user-invocable	true

blastn-vdb

Quick Start

• Command: blastn_vdb -query query.fa -db <SRA_or_WGS_name> [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blastn_vdb
• Full reference: See references/help.md

When To Use This Tool

• Run nucleotide BLAST directly against SRA or WGS-backed VDB data sources.
• Search sequencing reads or aligned reference sequences without first building a local BLAST DB.
• Control whether the search targets unaligned reads, aligned reference sequences, or both via -sra_mode.
• Keep a BLASTN-like workflow while operating in the VDB / SRA ecosystem.

Common Patterns

# 1) Search an accession's unaligned reads with tabular output
blastn_vdb \
  -query query.fa \
  -db SRR123456 \
  -sra_mode 0 \
  -outfmt 6 \
  -evalue 1e-10 \
  -num_threads 8

# 2) Search aligned reference sequences only
blastn_vdb \
  -query query.fa \
  -db SRR123456 \
  -sra_mode 1 \
  -out results.txt