Issues

• Lack of chromosome attribution for scaffolded assembly, but fewer inversions and overall better placement of contigs relative to the reference.

  malonge/RagTag#210 · Filter by author Ltressel opened on Mar 4, 2026

• Scaffolding within the same species

  malonge/RagTag#209 · Filter by author katiecdillon opened on Feb 14, 2026

• Ragtag scaffold inserted a uracil.

  malonge/RagTag#208 · Filter by author faulk-lab opened on Nov 22, 2025
  1

• RagTag overly sensitive when identifying minimap2 SAM format flag

  malonge/RagTag#207 · Filter by author ASLeonard opened on Oct 24, 2025
  1

• How to rename the scaffolds / Chromosomes?

  malonge/RagTag#206 · Filter by author nitinShukla1912 opened on Oct 2, 2025

• How to evaluate the results of newly assembled genomes

  malonge/RagTag#204 · Filter by author oganesson76 opened on Sep 5, 2025
  1

• Error with RagTag Scaffolding

  malonge/RagTag#203 · Filter by author neupanebpn63 opened on Jun 9, 2025

• overlook of strand information when connect two contig?

  malonge/RagTag#202 · Filter by author dukecomeback opened on Jun 6, 2025

• False positive for -a detection in --mm2-params when using --cap-kalloc option

  malonge/RagTag#201 · Filter by author JohGi opened on Jun 5, 2025

• Patch output files still incomplete

  malonge/RagTag#200 · Filter by author horvathdp opened on May 7, 2025
  2

• patch not producing ragtag.patch.fasta or apg file but gives no error mesg

  malonge/RagTag#199 · Filter by author horvathdp opened on May 6, 2025
  1

• Ragtag patch clarification

  malonge/RagTag#198 · Filter by author bmpaddy opened on Apr 22, 2025

• Ragtag correct --inter or --intra?

  malonge/RagTag#197 · Filter by author Samyuktha9624 opened on Apr 15, 2025

• can I find InDel and SNP from the output files?

  malonge/RagTag#196 · Filter by author waterhouseBenth opened on Mar 31, 2025

• Asking about ragtag patch runtime

  malonge/RagTag#195 · Filter by author Abieskawa opened on Mar 21, 2025

• The possibility of starting from HiFi ccs reads

  malonge/RagTag#192 · Filter by author OceanLyu opened on Nov 5, 2024

• integration with juicer

  malonge/RagTag#191 · Filter by author Overcraft90 opened on Oct 17, 2024

• question of Hi-C to resolve conflicts

  malonge/RagTag#189 · Filter by author njliangdong opened on Sep 18, 2024

• updategff produces wrong output if parts of the scaffolds are used in the AGP file

  malonge/RagTag#188 · Filter by author taprs opened on Sep 13, 2024

• RagTag error: "OSError: error when opening file"

  malonge/RagTag#187 · Filter by author ylzou867 opened on Sep 4, 2024
  1

• Missing ragtag.correct.reads.s.bam file

  malonge/RagTag#184 · Filter by author faye-romero opened on Jul 11, 2024
  1

• ragtag_scaffold.py: error: unrecognized arguments

  malonge/RagTag#182 · Filter by author athenasyarifa opened on Jun 24, 2024

• output file not found

  malonge/RagTag#181 · Filter by author Anysdn opened on Jun 20, 2024

• The scaffold command was submitted and the assembled result was not available

  malonge/RagTag#180 · Filter by author LZY19940813 opened on Jun 18, 2024
  1

• Using RagTag to close the gaps in a chromosome or reference genome using long-read data

  malonge/RagTag#179 · Filter by author gforg34 opened on Apr 8, 2024