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

# 3) Include filtered reads and cap hit count
blastn_vdb \
  -query query.fa \
  -db SRR123456 \
  -include_filtered_reads \
  -max_target_seqs 20 \
  -outfmt "6 qaccver saccver pident length evalue bitscore"

Recommended Workflow

1. Confirm the target accession or VDB source is available and that you really want SRA-backed search rather than a local BLAST database.
2. Set -sra_mode deliberately: 0 for unaligned reads, 1 for aligned reference sequences, 2 for both.
3. Use explicit -outfmt, -evalue, and -max_target_seqs settings so results remain predictable across runs.
4. Start with a small query set before scaling up to larger accession-backed searches.

Guardrails

• -db here is an SRA or WGS source name, not a standard local BLAST database path.
• The default task is megablast; override -task if you need blastn-short, dc-megablast, or another mode.
• Use BLAST+ style flags such as -help and -version; the usual --help pattern is wrong in this build.
• -num_descriptions and -num_alignments are incompatible with -max_target_seqs.
• -include_filtered_reads and -sra_mode can materially change the search universe, so record them in reproducible workflows.