A regression test suite and historical results for the Canu single molecule sequence assembler.
This is a set of scripts and configurations to compare results of Canu across different code points. The driver script will update a local copy of the canu github repo, checkout a specific version of Canu, and launch a (user-supplied) set of assemblies.
Each assembly will compare itself against a reference genome (using quast) and then compare quast results against a previously chosen curated assembly and report differences in the quast results.
The main driver is regression.pl. This will update the local repo, checkout a specific version of Canu, build, and then launch assemblies on the grid.
The "chosen curated assembly" can be updated using update-refasm.sh.
Nothing more than a list of special dates. It's quite out of date.
| Date | Hash | Milestone |
|---|---|---|
| 2020-10-16-1821 | 5638f7d9a5379373310ab62c28aa0cdbd864722d | Canu 2.1.1, branch v2.1-maintenance |
| 2020-09-18-1243 | b9826425676a2eb019fd2ad2f240f2eebd79c35a | mhap -minlength option |
| 2020-08-24-1052 | dd71f16d5c31e0f6d30297c215a9c62353079da9 | Canu 2.1, branch v2.1-maintenance |
| 2020-08-19-2326 | 7bb8a2435e3f8d2d9a73be44b2c9fef3cccd32a5 | Canu 2.1 master, (just after release) |
| 2020-07-22-1735 | afcb34fde3fb9445d57f8b311f92794f9c96baa5 | Build in 'build' instead of 'OSTYPE-MACHINETYPE'. (Regression might not work before this) |
| 2020-03-18-0351 | 541200a23245ebe71ad2b46f6d8f500431a1725e | Canu 2.0, branch v2.0-maintenance |
| --------------- | ---------------------------------------- | ------------------------------------------------------ |
| --------------- | ---------------------------------------- | ------------------------------------------------------ |
| 2018-09-18-0752 | trio support full run | |
| 2018-09-05-1307 | meryl v2 full run (complete) | |
| 2018-08-13-0800 | ||
| 2018-07-30-1450 | ||
| 2018-07-26-1654 | ||
| 2018-05-16-1124 | ||
| 2018-05-08-1454 | edlib patches | |
| 2018-05-04-0314 | last seqStore change RED fails, ran by hand (fixed on 05-05) |
|
| 2018-04-16-0545 | bogart bugs, after ovlStore bugs fixed FAILED - gkpStore partitioning (still) has bad BLOB pointers |
|
| 2018-03-28-1108 | before ovlStore changes FAILED - gkpStore partitioning has bad BLOB pointers |
|
| 2018-03-13-2009 | gkpStore changes FAILED - gkpStore partitioning has bad BLOB pointers |
|
| 2018-03-13-1715 | before gkpStore changes | |
| 2018-02-27-0846 | v1.7 | |
| --------------- | ---------------------------------------- | ------------------------------------------------------ |
| 2018-02-09-1146 | Use both read length and overlap length to filter evidence for correction. No change and I forget (in the two months it took to run it) what was exactly being tested. NOTE! These have BAD job sizes for RED, resulting in VERY VERY small jobs. |
|
| 2018-02-08-1804 | (before the next one) | |
| --------------- | ---------------------------------------- | ------------------------------------------------------ |
| 2017-08-14-1539 | v1.6 | |
| 2017-10-11-1435 | Minor bugfixes, new installation structure, | |
| 2017-10-05-2341 | One gkpStore. Pseudo-QV's for corrected reads. Output read names from mhap, not just per-job ID. Remove -w option from overlapInCore. |
|
| 2017-09-23-1710 | Bug fix; don't crash when no corrected sequence is generated for any read. | |
| 2017-09-22-1613 | Emit only single longest corrected read piece. Bug fixes in grid support. | |
| 2017-09-20-1513 | Bug fixes in overlap store histogram. | |
| 2017-09-18-1358 | Use corStore for correction. Estimate overlap scores; changes to overlap store stats data. Overlap scores are 16-bit integers. Fix inconsistent overlap scores introduced in last commit. |
|
| 2017-08-24-0051 | KNOWN BAD; overlap scores computed using inconsistent functions! Merge falcon_sense and input generation. |
|
| 2017-08-14-1539 | v1.6 (MISSING); just minor stuff since last commit. | |
| 2017-08-11-0829 | Minor logging change and bug fix. | |
| 2017-08-10-1830 | Bogart: dead bubble popping code removal, errorProfile memory optimization. | |
| 2017-08-02-0645 | Bug fixes. | |
| 2017-07-28-2128 | Bug fixes and intermediate file cleanup. | |
| 2017-07-25-2009 | ||
| 2017-07-03-1413 | ||
| 2017-06-29-1114 | ||
| 2017-06-09-1607 | ||
| 2017-06-07-1055 | ||
| 2017-05-19-1828 | ||
| 2017-05-10-1930 | ||
| --------------- | ---------------------------------------- | ------------------------------------------------------ |
| 2017-04-17-1531 | v1.5 | |
| 2017-03-10-0053 | alignPair rewrite | |
| 2017-03-10-0051 | alignPair rewrite, previous commit | |
| 2017-01-27-0903 | errorRate replacement | |
| 2017-01-27-0803 | errorRate replacement, previous commit | |
| 2017-01-06-0241 | stageDirectory (so nothing big will run before this) | |
| --------------- | ---------------------------------------- | ------------------------------------------------------ |
| 2016-12-12-2155 | v1.4 | |
| 2016-11-08-1117 | first that works | |
| 2016-11-07-1826 | adds support for onSuccess, but doesn't work | |
| --------------- | ---------------------------------------- | ------------------------------------------------------ |