ACCESS-CI allocation request — vertebrate all-to-all alignment

Working repository for an ACCESS-CI request to expand a completed all-to-all alignment of 581 Vertebrate Genomes Project (VGP) assemblies to a quality-controlled catalogue of publicly available vertebrate reference genomes.

The completed pilot comprises 336,980 ordered genome pairs computed on TACC Stampede3 under TG-MCB140147. Its interactive similarity and coverage atlas is available at https://unavailable-2374.github.io/vgp-heatmap/, and the workflow and related analyses are maintained in https://github.com/pangenome/lifetree.

Current draft

Drafts live in alignment-2026/.

Document	File	Page limit
Main Document	alignment-2026/main.md	10
Code Performance & Resource Costs	alignment-2026/perf.md	5
Curriculum Vitae	alignment-2026/cv/erik-garrison.md	2
References	alignment-2026/references.md	none
Special Requirements	alignment-2026/special-requirements.md	1
Abstract	alignment-2026/abstract.md	portal field
Open decisions	alignment-2026/CHECKLIST.md	n/a

Measured Stampede3 usage and the cost derivation imported from files.zip are kept in notes/alignment/usage-data-stampede3.md.

A reproducible NCBI survey dated 2026-08-01 found 14,247 current biological assemblies representing 6,358 vertebrate species across all assembly levels. See notes/alignment/ncbi-vertebrata-survey-2026-08-01.md. The multi-allocation Phase 1 universe is all 4,467 complete and chromosome- level assemblies representing 1,896 species. This request asks for 1M Stampede3 SUs to add approximately 800 assemblies in the next clade-balanced tranche. Later awards will complete Phase 1 and admit usable scaffold and contig assemblies.

Build

Markdown is converted to HTML with pandoc and printed to PDF with headless Chrome.

./build.sh                         # alignment request, draft notes visible
./build.sh --final                 # alignment request, TODO blocks removed
./build.sh main perf               # selected documents

PDFs and intermediate HTML are written to build/. Page limits are enforced by build.sh. A normal build renders paragraphs beginning with [TODO as orange draft notes. A final build removes them. SRC selects the document set and defaults to alignment-2026.

The automated build includes Erik Garrison's two-page CV from alignment-2026/cv/.

Repository layout

alignment-2026/    current vertebrate alignment request
notes/alignment/   imported measurements and cost basis
access.css         PDF stylesheet
build.sh           Markdown-to-PDF pipeline

Non-negotiable checks

• Do not invent assembly, usage, storage, or service-unit figures.
• Recompute ordered pairs as N(N−1) and incremental work beyond 581 as M(2×581 + M−1), where M=N−581.
• Reconcile the measured 10 TB working set with the approximately 1.5 TB compressed public PAF release before finalizing storage.
• Obtain approval to use work charged to TG-MCB140147 as preliminary results, and distinguish past work from the new request.
• Keep all submitted documents within their page limits.

Origin

This repository began as a copy of Anton Nekrutenko's ACCESS-CI allocation repository. That repository's earlier drafts and submission history are still present as galaxy-2026/ and archive/, exported verbatim from Google Drive. They are prior material and are not part of this request.