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CRISPRme+ 2.2.0-alpha.6

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@lucapinello lucapinello released this 14 Aug 02:43
· 81 commits to main since this release
v2.2.0-alpha.6
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Learn about vigilant mode.

CRISPRme+ is the next major version of CRISPRme (2.2.0) — variant-aware CRISPR off-target nomination, batteries included. Open alpha for beta testers. For production/clinical work, stay on the frozen CRISPRme 2.1.14.

Quickstart

docker pull pinellolab/crisprme:v2.2.0-alpha.6

Then follow the batteries-included quickstart — one download fetches the reference data and a ready-made variant-aware SpCas9 index (1000 Genomes + HGDP), so you can run a real off-target search immediately (no index build).

What's fixed in this release

This is the first alpha where a variant search on a batteries-included install works end-to-end (index-only download, no raw VCFs):

  • Batteries variant search (#7): the precomputed variant index now bundles its per-sample dictionaries, submit_job skips the redundant genome enrichment when a precomputed index is present, and the indel pipeline derives chromosomes from the bundled logs. A variant search no longer requires the multi-GB source VCFs.
  • crispritz v2.8.2 (#8, CRISPRitz#42): the -index search now ignores hidden metadata sidecars, so the SNP/variant search returns results instead of erroring with "only .bin files". Also bundles pigz for fast index publishing.
  • The hosted combined NGG_3_hg38+hg38_1000G_HGDP index was re-published with its dictionaries.

Validation

End-to-end genome-wide search on a real batteries install (downloaded index+dicts, no VCFs): enrichment skipped, precomputed index reused, SNP + variant + indel searches ran, post-analysis loaded the 152 GB dictionaries, full report + database built — 1,735 off-target sites produced. Also verified identical to a with-VCFs baseline on a chr22 harness.

Memory

16 GB is enough for a first run; the default genome-wide 1000G+HGDP variant search is memory-intensive — give Docker at least 32 GB (64 GB recommended).

🤖 Generated with Claude Code

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