Issues

• model-seq-err: FASTQ input is not structurally validated, so a non-FASTQ file yields a model

  bug
  ncsa/NEAT#341 · Filter by author joshfactorial opened on Sep 13, 2026

• apply_errors quality accounting has compensating off-by-ones, and blocks the remaining half of #335

  ncsa/NEAT#337 · Filter by author joshfactorial opened on Aug 29, 2026
  2

• research single cell simulation

  ncsa/NEAT#320 · Filter by author joshfactorial opened on Jun 26, 2026

• look into allelic dropout

  ncsa/NEAT#319 · Filter by author joshfactorial opened on Jun 26, 2026

• look into amplification bias

  ncsa/NEAT#318 · Filter by author joshfactorial opened on Jun 26, 2026

• model_sequencing_error: derive error transition/indel/insertion params from input FASTQ

  ncsa/NEAT#295 · Filter by author joshfactorial opened on May 19, 2026

• Integrate sub functions

  ncsa/NEAT#290 · Filter by author joshfactorial opened on May 19, 2026
  1

• specify an allele frequency

  ncsa/NEAT#289 · Filter by author joshfactorial opened on May 19, 2026

• CNV addition

  ncsa/NEAT#288 · Filter by author joshfactorial opened on May 19, 2026

• Copy number scripts

  ncsa/NEAT#226 · Filter by author keshav-gandhi opened on Dec 12, 2025