Rui Li

The output of braker.gff3 is missing "gene" feature

1

Hello dear developers, I want to use `braker.gff3` for downstream analysis, but the `gene` feature is missing when I use the `-gff3` parameter to output the gff file, and everything...

GeneMark version may be incompatible, resulting in train.f.gb format error

5

Hi dear developers, BRAKER is a powerful pipeline, but it often leads to compatibility issues. When I running the command `--genome merge_fix.fna --esmode --min_contig=10000 --cores 8 --AUGUSTUS_ab_initio --softmasking`, Braker has...

Huge storage occupation when running parallel tasks

1

Hi, I am running a parallel BRAKER2 pipeline on the cluster, and these tasks share the same protein file. When BRAKER2 is running, the process will consume a lot of...

Fix anchor name

1

**目标章节**：例如 1-js/01-getting-started/1-intro **当前上游最新 commit**：此处填写本项目英文版 https://github.com/javascript-tutorial/en.javascript.info 的最新 commit，例如 https://github.com/javascript-tutorial/zh.javascript.info/commit/b03ca00a992a73aaf213970e71f74ac1c04def33 **本 PR 所做更改如下：** 文件名 | 参考上游 commit | 更改（理由） -|-|- article.md | a23882d | 修改部分错误 > 注意，参考上游 commit 是指你所修改的文件，在英文仓库中同名文件的对应 commit，即你此次提交的修改的依据。如果本 PR 你只是提交一个文字或者语句优化，并非根据上游英文仓库的修改而提交的更新，则请填无。

only tools or research paper

1

Can we only include pangenome tools, or can research articles be added as well? I'd be happy to submit some PRs to document classic papers.

Can I use vclust to cluster bacterial sequences?

2

Thank you for developing such a convenient and powerful tool! I'm wondering why vclust emphasizes clustering viral sequences—can I use it for dereplicating bacterial sequences? Is it because viral sequences...