Issues

• Add HiCExplorer (hicQC) into the pipeline

  enhancement
  Plant-Food-Research-Open/assemblyqc#370 · Filter by author GallVp opened on Sep 14, 2026

• Add JCVI / MCscan (Python) into the pipeline

  enhancement
  Plant-Food-Research-Open/assemblyqc#369 · Filter by author GallVp opened on Sep 14, 2026

• Add Corgi into the pipeline

  enhancement
  Plant-Food-Research-Open/assemblyqc#368 · Filter by author GallVp opened on Sep 14, 2026
  

• Add Inspector into the pipeline

  enhancement
  Plant-Food-Research-Open/assemblyqc#367 · Filter by author GallVp opened on Sep 14, 2026

• Add GenomeScope2 + Smudgeplot into the pipeline

  enhancement
  Plant-Food-Research-Open/assemblyqc#366 · Filter by author GallVp opened on Sep 14, 2026

• Add QUAST / metaQUAST into the pipeline

  enhancement
  Plant-Food-Research-Open/assemblyqc#365 · Filter by author GallVp opened on Sep 14, 2026

• Add PSAURON into the pipeline

  enhancement
  Plant-Food-Research-Open/assemblyqc#364 · Filter by author GallVp opened on Sep 14, 2026
  1

• Add CRAQ into the pipeline

  enhancement
  Plant-Food-Research-Open/assemblyqc#319 · Filter by author CeciliaDeng opened on Nov 25, 2025
  

• Investigate calc_switchErr

  Plant-Food-Research-Open/assemblyqc#314 · Filter by author GallVp opened on Oct 10, 2025
  2

• Find a tool for mito/chloro sequence detection

  Plant-Food-Research-Open/assemblyqc#313 · Filter by author GallVp opened on Oct 7, 2025
  1

• add flagger?

  enhancement
  Plant-Food-Research-Open/assemblyqc#298 · Filter by author CeciliaDeng opened on Aug 22, 2025
  2

  

• [Project] Phasing approaches for consideration

  enhancement
  Plant-Food-Research-Open/assemblyqc#261 · Filter by author CeciliaDeng opened on Jul 16, 2025
  2

• HiC PDF report size on the AssemblyQC/HIC is very small

  bugwontfix
  Bug

  Plant-Food-Research-Open/assemblyqc#221 · Filter by author GallVp opened on Jun 6, 2025 · 3.0.0
  2

  

• Investigate phasedWgsVsSNP

  Plant-Food-Research-Open/assemblyqc#213 · Filter by author GallVp opened on May 22, 2025 · 3.0.0

• Add extra parameters for MUMme/Circos/dotplot workflow

  documentationenhancementhelp wanted
  Plant-Food-Research-Open/assemblyqc#182 · Filter by author CeciliaDeng opened on Nov 20, 2024 · 3.0.0
  7

• Kraken2 DB: missing pyrus

  bug
  Plant-Food-Research-Open/assemblyqc#181 · Filter by author CeciliaDeng opened on Nov 19, 2024 · 3.0.0
  1

• Enquiry: Kraken2 result. Pear sequences tagged as apple

  bug
  Plant-Food-Research-Open/assemblyqc#169 · Filter by author CeciliaDeng opened on Oct 29, 2024 · 3.0.0
  4

• Add compleasm

  enhancement
  Plant-Food-Research-Open/assemblyqc#127 · Filter by author christinawu2008 opened on Sep 16, 2024
  5

• Can we automatically label sequences for PLOTSR?

  enhancement
  Plant-Food-Research-Open/assemblyqc#116 · Filter by author GallVp opened on Jul 24, 2024
  1

• [UPDATE] GITHUB/NCBI/FCS -> 0.5.4

  enhancement
  Plant-Food-Research-Open/assemblyqc#114 · Filter by author GallVp opened on Jul 24, 2024
  2

  

• [UPDATE] GITHUB/PYTHON/CPYTHON -> 3.12.4

  enhancement
  Plant-Food-Research-Open/assemblyqc#113 · Filter by author GallVp opened on Jul 24, 2024

• [UPDATE] GITHUB/OUSHUJUN/EDTA -> 2.2.0

  enhancement
  Plant-Food-Research-Open/assemblyqc#112 · Filter by author GallVp opened on Jul 24, 2024

• [UPDATE] GITHUB/SHENWEI356/SEQKIT -> 2.8.2

  enhancement
  Plant-Food-Research-Open/assemblyqc#109 · Filter by author GallVp opened on Jul 23, 2024

• [UPDATE] GITHUB/NCBI/SRA-TOOLS -> 3.1.1

  enhancement
  Plant-Food-Research-Open/assemblyqc#108 · Filter by author GallVp opened on Jul 23, 2024

• BlobTools

  enhancement
  Plant-Food-Research-Open/assemblyqc#90 · Filter by author GallVp opened on Jun 1, 2024
  1