# Feature/Pull Request **URL:** https://forum.biobakery.org/c/pull-request/featurepull-request/40.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [About the Feature/Pull Request category](https://forum.biobakery.org/t/about-the-feature-pull-request-category/3120)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 0
We welcome feedback and issue reporting for all bioBakery tools through our Discourse site. For users that would like to directly contribute to the tools we are happy to field PRs to address bug fixes. Please note the tu… --- ## [Feature request: allow to put fraction with some parameters](https://forum.biobakery.org/t/feature-request-allow-to-put-fraction-with-some-parameters/8231)
**Author:** [@Alexiy\_Boyko](https://forum.biobakery.org/u/Alexiy_Boyko)\ **Replies:** 0\ **Last updated:** [July 4, 2025, 10:09am UTC](https://forum.biobakery.org/t/feature-request-allow-to-put-fraction-with-some-parameters/8231 "2025-07-04T10:09:19Z")
v3.3.1 Is I don’t know about my species, it genus, number of markers within their genomes, quality of their genomes, or number of markers at database, but I don’t want include in analysis genomes with high number of mis… --- ## [Feature request: phylophlan\_write\_config\_file, force generation of config, despite the lack of a program at PATH](https://forum.biobakery.org/t/feature-request-phylophlan-write-config-file-force-generation-of-config-despite-the-lack-of-a-program-at-path/8230)
**Author:** [@Alexiy\_Boyko](https://forum.biobakery.org/u/Alexiy_Boyko)\ **Replies:** 0\ **Last updated:** [July 4, 2025, 9:59am UTC](https://forum.biobakery.org/t/feature-request-phylophlan-write-config-file-force-generation-of-config-despite-the-lack-of-a-program-at-path/8230 "2025-07-04T09:59:49Z")
v3.1.1 If I have non-standard binary name or hasn’t binary at PATH, I also want to can create the config file. I am using phylophlan for the first time and yesterday the behavior of this script caused me a lot of pain. … --- ## [Support for SummarizedExperiment assays](https://forum.biobakery.org/t/support-for-summarizedexperiment-assays/7772)
**Author:** [@antagomir](https://forum.biobakery.org/u/antagomir)\ **Replies:** 3\ **Last updated:** [January 31, 2025, 6:19pm UTC](https://forum.biobakery.org/t/support-for-summarizedexperiment-assays/7772 "2025-01-31T18:19:48Z")
Maaslin3 0.99.3 Thanks for adding SummarizedExperiment support for Maaslin3, and soon Bioconductor availability. SummarizedExperiment supports multiple abundance tables (e.g. counts, relative abundances, log, clr etc) … --- ## [KneadData setup.py update to URL reference for TRF.exe](https://forum.biobakery.org/t/kneaddata-setup-py-update-to-url-reference-for-trf-exe/7576)
**Author:** [@Kborg000](https://forum.biobakery.org/u/Kborg000)\ **Replies:** 0\ **Last updated:** [November 11, 2024, 9:09pm UTC](https://forum.biobakery.org/t/kneaddata-setup-py-update-to-url-reference-for-trf-exe/7576 "2024-11-11T21:09:52Z")
In the GitHub repository for KneadData, the setup.py script references two URLs for retrieving the TRF executable download on lines #246 & 248 (shown below). trf\_exe = “trf” if mac\_os: url = "http://tandem.bu.edu/t… --- ## [Multithreading blasting of unaligned reads](https://forum.biobakery.org/t/multithreading-blasting-of-unaligned-reads/7349)
**Author:** [@rroutsong](https://forum.biobakery.org/u/rroutsong)\ **Replies:** 1\ **Last updated:** [August 13, 2024, 2:36pm UTC](https://forum.biobakery.org/t/multithreading-blasting-of-unaligned-reads/7349 "2024-08-13T14:36:08Z")
humann v3.9 Running data with humann3 with many unaligned reads increases the time of execution significantly. Recently I have used cProfiler to show that this time is primarily spent in the unaligned blastx portion of … --- ## [Performance of HUMAnN Custom Database Creation](https://forum.biobakery.org/t/performance-of-humann-custom-database-creation/7091)
**Author:** [@ChristianRomberg](https://forum.biobakery.org/u/ChristianRomberg)\ **Replies:** 2\ **Last updated:** [June 20, 2024, 9:03pm UTC](https://forum.biobakery.org/t/performance-of-humann-custom-database-creation/7091 "2024-06-20T21:03:46Z")
Hi, I am currently in the process of writing my bachelor thesis and I am using HUMAnN3 in the process. I noticed that the custom database creation step is quite slow for what is seems to be doing and decided to profile … --- ## [Reduce storage requirements when running HUMAnN](https://forum.biobakery.org/t/reduce-storage-requirements-when-running-humann/3642)
**Author:** [@alienzj](https://forum.biobakery.org/u/alienzj)\ **Replies:** 1\ **Last updated:** [May 26, 2022, 10:13am UTC](https://forum.biobakery.org/t/reduce-storage-requirements-when-running-humann/3642 "2022-05-26T10:13:59Z")
PR: