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CRISPRme+ 2.2.0-alpha.8

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@lucapinello lucapinello released this 14 Aug 04:54
· 77 commits to main since this release
v2.2.0-alpha.8
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Learn about vigilant mode.

CRISPRme+ 2.2.0 open alpha — variant-aware CRISPR off-target nomination, batteries included. For production/clinical work use the frozen CRISPRme 2.1.14.

Quickstart

docker pull pinellolab/crisprme:v2.2.0-alpha.8

Then follow the batteries-included quickstart. Note: the batteries install needs ≈250 GB free disk (~44 GB download that expands to ~190 GB — the per-sample variant dictionaries are large) and 32 GB RAM (64 GB recommended) for the genome-wide variant search.

Changes since alpha.6

  • Annotations ON by default (alpha.7): the built-in ENCODE cCREs (SCREEN) + DHS + GENCODE bundle now surfaces on a fresh install (the download ships it bgzipped; the option-check accepted only the unzipped form, so searches ran unannotated). It's now selected by default.
  • Maximum-edits slider floored at 1 (alpha.8): 0 was a niche exact-matches-only mode that hit a crispritz --max-edits 0 bug (empty result on large indexes). The on-target (0 edits) is still reported at any setting (Total 0 ≤ 1), so nothing useful is lost.
  • (alpha.7 also bundled pigz and shipped crispritz v2.8.2, whose -index search ignores hidden metadata sidecars — fixing the empty SNP/variant result on the batteries index.)

Upgrading

If you installed the combined index before this line, re-download it so it includes the per-sample dictionaries:

rm -rf <data>/genome_library/NGG_3_hg38+hg38_1000G_HGDP*  <data>/Dictionaries/*hg38_1000G_HGDP
docker run --rm -v "<data>:/DATA" -w /DATA pinellolab/crisprme:v2.2.0-alpha.8 \
  crisprme.py download --what index --index-name NGG_3_hg38+hg38_1000G_HGDP --path /DATA

🤖 Generated with Claude Code

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