breseq is a computational pipeline for finding mutations relative to a reference sequence using high-throughput DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
active 2023-08-29 → 2026-08-14 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 1082 days from 2023-08-29 to 2026-08-14. Pushes: 55 total, peak 3 in a day. Pull requests: 5 total, peak 2 in a day. Issues: 52 total, peak 8 in a day. Comments: 82 total, peak 6 in a day. Stars: 31 total, peak 1 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 |
|---|---|---|---|---|
| jeffreybarrick | 135 | 55 | 4 | 49 |
| Hocnonsense | 4 | 0 | 0 | 2 |
| ankane | 4 | 0 | 0 | 2 |
| gabypetrungaro | 4 | 0 | 0 | 2 |
| leowill01 | 3 | 0 | 0 | 2 |
| nspahr08 | 3 | 0 | 0 | 2 |
| padpadpadpad | 3 | 0 | 0 | 2 |
| dannagifford | 3 | 0 | 0 | 2 |
| Avylab | 3 | 0 | 0 | 2 |
| spleonard1 | 2 | 0 | 0 | 1 |
| Gia1120 | 2 | 0 | 0 | 1 |
| HongAnTechnician | 2 | 0 | 0 | 1 |
| rowi2024 | 2 | 0 | 0 | 1 |
| ThomasHindre | 2 | 0 | 0 | 2 |
| he-hai | 2 | 0 | 0 | 2 |
| zahraa992 | 1 | 0 | 0 | 0 |
| erikwolfsohn | 1 | 0 | 0 | 1 |
| valery-shap | 1 | 0 | 0 | 0 |
| miniluphy | 1 | 0 | 0 | 0 |
| mikeblazanin | 1 | 0 | 0 | 0 |
Recent activity
Latest issues, pull requests and releases
- Pull request#418jeffreybarrick2026-06-28 11:39
- Issue comment#409dannagifford2026-03-21 03:52Best practices for reducing potential false positives in polymorphism mode?
- Issue#409mikeblazanin2026-03-20 22:48Best practices for reducing potential false positives in polymorphism mode?
- Issue#408jeffreybarrick2026-02-16 19:52Hybrid reads
- Issue comment#408jeffreybarrick2026-02-12 17:37Hybrid reads
- Issue#407zhliUU2026-01-14 14:57BreSeq as nf-core modules
- Issue comment#403jeffreybarrick2025-12-11 21:20Documentation "-p" option
- Issue#403jeffreybarrick2025-12-11 21:20Documentation "-p" option
- Issue comment#406nspahr082025-12-09 03:11Which bam to use for calculating coverage from all mappable reads?
- Issue comment#406nspahr082025-12-08 16:05Which bam to use for calculating coverage from all mappable reads?
- Issue#406nspahr082025-12-02 16:25Which bam to use for calculating coverage from all mappable reads?
- Issue comment#405jeffreybarrick2025-11-10 12:18Links in index.html direct to wrong results
- Issue comment#405sennihu2025-11-10 12:16Links in index.html direct to wrong results
- Issue#403kullrich2025-09-12 08:52Documentation "-p" option
- Issue#402jpgoldberg2025-09-07 21:21configure ignores `--with-static-zlib` (with proposed solution)
- Issue comment#395abrozzi2025-08-25 07:34GDTools COMPARE TSV output headers can vary
- Issue#401jeffreybarrick2025-08-06 21:30FATAL ERROR & STACK TRACE ERROR in breseq
- Issue comment#401IshaR982025-08-06 09:45FATAL ERROR & STACK TRACE ERROR in breseq
- Issue comment#400bhukrit2025-07-14 15:24truncated file. Aborting error from samtool step
- Issue comment#392gabypetrungaro2025-06-14 18:41differences in JC evidence when comparing annotated.gd files with the corresponding .html files
- Issue#399jeffreybarrick2025-06-14 16:06Remove internal samtools/htslib compile
- Issue comment#234jeffreybarrick2025-06-14 15:44Stale reference and reads
- Issue#234jeffreybarrick2025-06-14 15:44Stale reference and reads
- Issue#272jeffreybarrick2025-06-14 15:43Empty allele in VCF output
- Issue comment#275jeffreybarrick2025-06-14 15:43Rename output.gd file with the name of the fastq file or part of it
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 31 stars here means stars gained during the window, not the repo's star count.