Core

Log

Generated 2026-04-12 07:16 UTC

[2026-04-07] setup | Workspace initialized

  • Seeded the repository structure for an LLM-maintained research wiki.
  • Added AGENTS.md, README.md, and scripts/wiki.py.

[2026-04-07 09:38 KST] query created | compare retrieval strategies

  • Created query page wiki/queries/20260407_093832_compare-retrieval-strategies.md.

[2026-04-07 09:46 KST] ingest queued | Multi-platform discovery of haplotype-resolved structural variation in human genomes

  • Registered raw source raw/sources/2019_chaisson_multi-platform-haplotype-resolved-structural-variation-human-genomes.pdf.
  • Created source page wiki/sources/2019_chaisson_multi-platform-haplotype-resolved-structural-variation-human-genomes.md.

[2026-04-07 09:46 KST] ingest queued | Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology

  • Registered raw source raw/sources/2022_otsuki_trio-structural-variation-panel-activated-t-lymphocytes.pdf.
  • Created source page wiki/sources/2022_otsuki_trio-structural-variation-panel-activated-t-lymphocytes.md.

[2026-04-07 09:46 KST] ingest queued | Approaches to long-read sequencing in a clinical setting to improve diagnostic rate

  • Registered raw source raw/sources/2022_sanford-kobayashi_clinical-long-read-diagnostic-rate.pdf.
  • Created source page wiki/sources/2022_sanford-kobayashi_clinical-long-read-diagnostic-rate.md.

[2026-04-07 09:46 KST] ingest queued | Long-read whole-genome analysis of human single cells

  • Registered raw source raw/sources/2023_hard_long-read-whole-genome-analysis-human-single-cells.pdf.
  • Created source page wiki/sources/2023_hard_long-read-whole-genome-analysis-human-single-cells.md.

[2026-04-07 09:46 KST] ingest queued | Utility of long-read sequencing for All of Us

  • Registered raw source raw/sources/2024_mahmoud_utility-long-read-sequencing-all-of-us.pdf.
  • Created source page wiki/sources/2024_mahmoud_utility-long-read-sequencing-all-of-us.md.

[2026-04-07 09:46 KST] ingest queued | Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data

  • Registered raw source raw/sources/2024_kosugi_comparative-evaluation-short-vs-long-read-variants.pdf.
  • Created source page wiki/sources/2024_kosugi_comparative-evaluation-short-vs-long-read-variants.md.

[2026-04-07 09:46 KST] ingest queued | Long-read genome sequencing resolves complex genomic rearrangements in rare genetic syndromes

  • Registered raw source raw/sources/2024_showpnil_long-read-genome-sequencing-complex-rearrangements-rare-syndromes.pdf.
  • Created source page wiki/sources/2024_showpnil_long-read-genome-sequencing-complex-rearrangements-rare-syndromes.md.

[2026-04-07 09:46 KST] ingest queued | Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility

  • Registered raw source raw/sources/2025_gong_long-read-sequencing-945-han-individuals.pdf.
  • Created source page wiki/sources/2025_gong_long-read-sequencing-945-han-individuals.md.

[2026-04-07 09:46 KST] ingest queued | Long read sequencing enhances pathogenic and novel variation discovery in patients with rare diseases

  • Registered raw source raw/sources/2025_sinha_long-read-sequencing-rare-diseases.pdf.
  • Created source page wiki/sources/2025_sinha_long-read-sequencing-rare-diseases.md.

[2026-04-07 09:46 KST] ingest queued | Structural variation in 1,019 diverse humans based on long-read sequencing

  • Registered raw source raw/sources/2025_schloissnig_structural-variation-1019-diverse-humans-long-read-sequencing.pdf.
  • Created source page wiki/sources/2025_schloissnig_structural-variation-1019-diverse-humans-long-read-sequencing.md.

[2026-04-07 09:48 KST] corpus curated | Long Read WGS starter corpus

  • Added a 10-paper starter corpus synthesis page.
  • Updated the overview with the current Long Read WGS collection scope.

[2026-04-07 09:53 KST] corpus normalized | Long Read WGS filenames and spreadsheet

  • Renamed 10 PDF files to the first_author_year_first5words.pdf convention.
  • Saved spreadsheet long_read_wgs_papers.xlsx.
  • Updated source page raw file references to the renamed PDFs.

[2026-04-07 10:10 KST] deep ingest | Long Read WGS source pages and concepts

  • Deep-ingested all 10 source pages with study design, key findings, strengths, caveats, and concept links.
  • Added 6 concept pages covering structural variation, platform tradeoffs, rare disease diagnostics, population SV atlases, and hard genomic regions.
  • Updated the overview, index, and corpus synthesis to reflect the current cross-paper claims and open tensions.