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@quwubin quwubin released this 13 Jul 15:41
v4.3.1
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MFEprimer v4.3.1

Smaller primer-QC indexes for large genomes, without changing QC / specificity semantics.

Highlights

  • New default binary index (.primerqc.bin)
    Exact 9-mer indexing for primer 3' ends is unchanged. The new format stores each reference window once and recovers minus-strand hits at query time, so plus/minus results stay consistent with previous releases.

  • Much smaller indexes than the legacy text format
    Especially helpful for large reference genomes where the old .primerqc indexes could become extremely large.

  • mfeprimer migrate
    Batch-upgrade existing legacy indexes under a directory to the new binary format.
    Optional --verify. --delete removes legacy text sidecars only after a successful upgrade.

  • Existing databases keep working. Rebuild / migrate when you want the smaller footprint.

Updates (same version, refreshed binaries)

  • *.spec.tsv: add productTm and ta columns (same values as the text report’s ProductTm / Ta). See issue #32.

Quick start

mfeprimer index -i reference.fa -c 16 -f
mfeprimer migrate -d /path/to/databases --verify

Notes

  • For very large assemblies, please compare index size (du -h) and peak memory on your own FASTA and report back if anything still looks off.
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