Tools for fast and flexible genome assembly scaffolding and improvement
active 2023-08-15 → 2026-04-08 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 968 days from 2023-08-15 to 2026-04-08. Pushes: 0 total, peak 0 in a day. Pull requests: 0 total, peak 0 in a day. Issues: 21 total, peak 2 in a day. Comments: 35 total, peak 3 in a day. Stars: 97 total, peak 3 in a day.
- Pushes
- Pull requests
- Issues
- Comments
- Stars
Stars, PRs, issues and forks are under-captured in the later part of this window. GH Archive progressively stopped capturing non-push events during 2026 — −95% or worse by the end of the window. Every series here except Pushes fades for that reason, so a decline above reflects the archive, not this repository. Pushes stay reliable throughout, so read them, and the contributor counts derived from them, as the real signal. Data health has the measurements.
Top contributors
Pushes, PRs, issues, reviews and comments — stars and forks excluded, so this is contribution rather than popularity
| Contributor | Contributions | Pushes | PRs | Comments |
|---|---|---|---|---|
| nvuhunganh | 3 | 0 | 0 | 1 |
| taprs | 3 | 0 | 0 | 3 |
| hrpelg | 3 | 0 | 0 | 2 |
| adadiehl | 2 | 0 | 0 | 1 |
| juusotas | 2 | 0 | 0 | 2 |
| mabh5 | 2 | 0 | 0 | 1 |
| dannagifford | 2 | 0 | 0 | 2 |
| faulk-lab | 2 | 0 | 0 | 1 |
| malonge | 2 | 0 | 0 | 2 |
| nickgladman | 2 | 0 | 0 | 2 |
| shivanshss | 2 | 0 | 0 | 2 |
| mschatz | 2 | 0 | 0 | 2 |
| dtusso2020 | 2 | 0 | 0 | 2 |
| arif-tanmoy | 2 | 0 | 0 | 0 |
| jarbsonsilva | 1 | 0 | 0 | 1 |
| Yogesh1-11 | 1 | 0 | 0 | 1 |
| karthickbrlab | 1 | 0 | 0 | 0 |
| faye-romero | 1 | 0 | 0 | 0 |
| waterhouseBenth | 1 | 0 | 0 | 0 |
| DustinSokolowski | 1 | 0 | 0 | 1 |
Recent activity
Latest issues, pull requests and releases
- Issue#210Ltressel2026-03-04 15:38Lack of chromosome attribution for scaffolded assembly, but fewer inversions and overall better placement of contigs relative to the reference.
- Issue comment#208faulk-lab2025-11-22 18:50Ragtag scaffold inserted a uracil.
- Issue#208faulk-lab2025-11-22 17:50Ragtag scaffold inserted a uracil.
- Issue comment#175DustinSokolowski2025-11-03 17:20patch output genome is identical to input target genome
- Issue#206nitinShukla19122025-10-02 05:29How to rename the scaffolds / Chromosomes?
- Issue comment#204mschatz2025-09-08 01:18How to evaluate the results of newly assembled genomes
- Issue#204oganesson762025-09-05 15:38How to evaluate the results of newly assembled genomes
- Issue comment#146matthew-pumc2025-04-27 02:42Error message when running ragtag_scaffold.py
- Issue#198bmpaddy2025-04-22 02:28Ragtag patch clarification
- Issue#196waterhouseBenth2025-03-31 00:28can I find InDel and SNP from the output files?
- Issue comment#132dtusso20202025-03-15 03:15RagTag.py merge
- Issue comment#82dtusso20202025-03-15 02:15Error using merge
- Issue comment#187xubiy2025-01-14 02:08RagTag error: "OSError: error when opening file"
- Issue#193karthickbrlab2025-01-07 06:22error during scaffolding..unable to get scaffold.fasta
- Issue comment#166juusotas2024-12-30 12:58updategff issues
- Issue comment#23juusotas2024-12-07 11:09Unable to update gff
- Issue comment#131jarbsonsilva2024-12-06 22:42Can I use RegTag for placing scaffold of a closely related on chromosomes using a reference genome of chromosome scale
- Issue#190arif-tanmoy2024-09-29 05:39Scaffold option -r error
- Issue#190arif-tanmoy2024-09-29 05:25Scaffold option -r error
- Issue comment#185adadiehl2024-09-11 14:01ragtag.patch.fasta lacks unplaced contigs?
- Issue#185adadiehl2024-09-11 14:01ragtag.patch.fasta lacks unplaced contigs?
- Issue comment#132awesomedeer2024-08-29 06:39RagTag.py merge
- Issue#186mrvollger2024-07-30 19:54Adjust default gap size
- Issue comment#141dannagifford2024-07-19 07:50a bytes-like object is required, not 'dict'
- Issue comment#155dannagifford2024-07-19 07:46RagTag patch bug
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 97 stars here means stars gained during the window, not the repo's star count.