Blastn Vdb

# 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.