Issues

• chromosomal assignment after running yahs

  c-zhou/yahs#123 · Filter by author okendojo opened on Oct 19, 2026
  1

• Thoughts on using OmniC pipeline with Arima data

  c-zhou/yahs#121 · Filter by author V-JJ opened on Nov 23, 2025

• Why did the QV value decrease significantly after using YAHS for HiC scaffolding?

  c-zhou/yahs#120 · Filter by author JieQYan opened on Nov 20, 2025
  4

• telo-motif option not in docker image

  c-zhou/yahs#119 · Filter by author Artifice120 opened on Aug 27, 2025

• Which bam generated from HiC-Pro should be fed to yahs

  c-zhou/yahs#118 · Filter by author leon945945 opened on May 30, 2025
  5

• Alternate assembly has better scaffold N50 stats than primary assembly

  c-zhou/yahs#117 · Filter by author afiyachida opened on May 27, 2025

• Initial input as scaffolds?

  c-zhou/yahs#116 · Filter by author ejc043 opened on May 27, 2025

• Add an option to accept black contig/region list

  c-zhou/yahs#115 · Filter by author xiekunwhy opened on Apr 28, 2025

• Scaffolding genomes with lots of repeat elements

  c-zhou/yahs#114 · Filter by author jomhoff opened on Apr 11, 2025

• when generate hic contact map, why you produce a alignments_sorted.txt.part file then rename it to alignments_sorted.txt afterwords.

  c-zhou/yahs#112 · Filter by author dukecomeback opened on Apr 11, 2025

• Telomeric repeats in first scaffold

  c-zhou/yahs#111 · Filter by author diana-moreno-santillan opened on Apr 11, 2025

• issue with PoreC based scaffolding

  c-zhou/yahs#110 · Filter by author dasn588 opened on Feb 14, 2025
  2

• telo motif

  c-zhou/yahs#109 · Filter by author tamsinlh opened on Feb 5, 2025
  1

• gaps

  c-zhou/yahs#106 · Filter by author rsandean opened on Jan 2, 2025
  3

• Sorted by names vs sorted by coordinates

  c-zhou/yahs#101 · Filter by author cruzreyc opened on Dec 3, 2024
  1

• re-scaffolding using agp file

  c-zhou/yahs#100 · Filter by author amara86 opened on Dec 2, 2024
  1

• Issues with resolution

  c-zhou/yahs#99 · Filter by author hw85241 opened on Nov 24, 2024
  1

• Question about the mapping process for yahs

  c-zhou/yahs#98 · Filter by author ericgonzalezs opened on Nov 6, 2024
  2

• Issue with Juicer Tools Preprocessing

  c-zhou/yahs#96 · Filter by author yeyu52 opened on Oct 5, 2024
  1

• There is no longer a need to manually set the scale factor in Juicebox

  c-zhou/yahs#94 · Filter by author zengxiaofei opened on Aug 26, 2024
  18

• YAHS merges two chromosomes in alternate haplotype

  c-zhou/yahs#88 · Filter by author MboiTui opened on Jun 4, 2024
  7

• Scaffolding by yahs introduces 200 bp gaps in the assembly

  c-zhou/yahs#87 · Filter by author janina-rinke opened on Apr 23, 2024
  3

• Juicer files only allow manual curation of first scaffold in JBAT

  c-zhou/yahs#86 · Filter by author rsandean opened on Apr 16, 2024
  2

• Unexpected Zero Reads Pairs and Output Size with yahs and Juicer Preprocessing Pipeline

  c-zhou/yahs#85 · Filter by author Hanjiangna opened on Apr 16, 2024
  4

• The question about regenerating a HiC contact map for the final assembly

  c-zhou/yahs#84 · Filter by author qdu-beep opened on Mar 8, 2024