Detecting contamination in NGS data and multi-species analysis
active 2023-08-15 → 2026-01-09 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 879 days from 2023-08-15 to 2026-01-09. Pushes: 4 total, peak 3 in a day. Pull requests: 3 total, peak 1 in a day. Issues: 23 total, peak 4 in a day. Comments: 25 total, peak 2 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 |
|---|---|---|---|---|
| StevenWingett | 29 | 4 | 1 | 16 |
| Linnaeus001 | 5 | 0 | 0 | 3 |
| Ayush09-cmd | 4 | 0 | 0 | 2 |
| ag1805x | 2 | 0 | 0 | 0 |
| keenhl | 2 | 0 | 0 | 1 |
| EDH0216 | 2 | 0 | 0 | 1 |
| mp15 | 1 | 0 | 1 | 0 |
| PietroD | 1 | 0 | 0 | 0 |
| kuanyili | 1 | 0 | 0 | 0 |
| SergeWielhouwer | 1 | 0 | 0 | 0 |
| LauraEgolf | 1 | 0 | 0 | 0 |
| HenriettaHolze | 1 | 0 | 0 | 0 |
| sandratra-rab | 1 | 0 | 0 | 1 |
| chrismitbiz | 1 | 0 | 0 | 1 |
| lightning-auriga | 1 | 0 | 1 | 0 |
| Eduardo-Auer | 1 | 0 | 0 | 0 |
| johnstonmj | 1 | 0 | 0 | 0 |
Recent activity
Latest issues, pull requests and releases
- Issue comment#83StevenWingett2026-01-09 16:14fastq_screen --get_genomes download failure
- Issue comment#82StevenWingett2025-08-11 08:59wget is an optional requirement
- Issue comment#80StevenWingett2025-07-04 08:53Extend minimap2 compatibility; add support for user-configured gzip alternatives
- Pull request#80lightning-auriga2025-06-11 13:06
- Issue comment#79EDH02162025-05-16 16:15get_genomes not finding the correct filepath to the prebuilt genomes online
- Issue comment#79StevenWingett2025-05-16 16:05get_genomes not finding the correct filepath to the prebuilt genomes online
- Issue#79EDH02162025-05-16 14:34get_genomes not finding the correct filepath to the prebuilt genomes online
- Issue#78ag1805x2025-01-13 07:28Genome location
- Issue comment#77StevenWingett2025-01-10 18:07Interpreting ribosomal RNA contamination
- Issue#78ag1805x2025-01-09 11:56Genome location
- Issue#77PietroD2024-11-14 17:31Interpreting ribosomal RNA contamination
- Issue comment#76sandratra-rab2024-11-08 15:15no minimap2 index was found
- Issue#76johnstonmj2024-11-06 19:34no minimap2 index was found
- Issue comment#75StevenWingett2024-11-04 10:41FastQ-Screen does not recognize BWA index file with ".64" extension
- Issue#75LauraEgolf2024-10-10 18:25FastQ-Screen does not recognize BWA index file with ".64" extension
- Issue comment#74StevenWingett2024-10-01 15:36Minimap2 aligner, only support for fa.gz/.fa files instead of mmi index files
- Issue#74StevenWingett2024-10-01 15:36Minimap2 aligner, only support for fa.gz/.fa files instead of mmi index files
- Issue#74SergeWielhouwer2024-10-01 11:46Minimap2 aligner, only support for fa.gz/.fa files instead of mmi index files
- Issue#72StevenWingett2024-09-27 11:25Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137
- ReleaseStevenWingett2024-09-20 11:22FastQ Screen v0.16.0
- Pull request#67StevenWingett2024-09-20 09:46
- Issue comment#72Ayush09-cmd2024-09-13 15:03Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137
- Issue comment#72StevenWingett2024-09-13 11:10Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137
- Issue comment#73Ayush09-cmd2024-09-12 06:09fastq screen is not screening against the added genome
- Issue#73Ayush09-cmd2024-09-12 06:08fastq screen is not screening against the added genome
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.