Makembindex

makembindex

Quick Start

• Command: makembindex -input <db_or_fasta> -output <index_prefix> [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/makembindex
• Full reference: See references/help.md

When To Use This Tool

• Build a BLAST database index as an explicit performance or infrastructure step.
• Tune index construction parameters such as -nmer, -stride, -volsize, or -ws_hint.
• Generate an index from either an existing BLAST DB or FASTA input, depending on -iformat.
• Inspect available masking filters with -show_filters before using -db_mask.

Common Patterns

# 1) Build an index from an existing BLAST database
makembindex \
  -input nt \
  -iformat blastdb \
  -output nt.mbidx

# 2) Dry-run a custom index configuration
makembindex \
  -input ref.fa \
  -iformat fasta \
  -output ref.mbidx \
  -nmer 12 \
  -stride 4 \
  -dryrun

# 3) List masking filters available in the source BLAST DB
makembindex \
  -input nt \
  -show_filters

Recommended Workflow

1. Decide whether the source is a BLAST database or FASTA and set -iformat deliberately.
2. Start with a conservative index build, then only tune -nmer, -stride, -volsize, or -ws_hint if you have a concrete search-performance reason.
3. Use -dryrun first when testing parameters on large databases.
4. Keep the index artifacts alongside the database they were built from and rebuild them if the underlying DB changes.

Guardrails

• This is an advanced BLAST infrastructure tool, not a routine prerequisite for every BLAST database.
• -output is incompatible with -show_filters.
• -db_mask requires -input and only makes sense when the source DB actually carries masking metadata.
• -legacy and -old_style_index are compatibility switches; do not enable them casually.
• Use BLAST+ flag style such as -help and -version, not --help.