compleasm

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arthropoda_odb10 same BUSCOs for multiple assemblies

4

Hello, I am running this script: [SCRIPT_NCBI_quast_compleasm_20240413_v1.txt](https://github.com/huangnengCSU/compleasm/files/15004465/SCRIPT_NCBI_quast_compleasm_20240413_v1.txt) And getting this output: [quast_compleasm_27733587.txt](https://github.com/huangnengCSU/compleasm/files/15004512/quast_compleasm_27733587.txt) In short, for every different assembly I am getting the exact same BUSCO scores. Please let me know...

katiecdillon

Feature request: BUSCO-formatted output

1

Thanks for the awesome tool! This is more a feature request - if the goal is to have a better/faster version of BUSCO, it would be helpful if the outputs...

schorlton

I'm using protein mode compleasm in the BRAKER 3.08 pipeline and have a script to annotate the BUSCOs in the braker.gff3 output. I've found the counts do not quite agree...

jbh-cas

Hi, That's a good tool. I used the tool and BUSCO to value my gene models. However, the results is slightly different, especially duplicated genes. BUSCO results： # BUSCO was...

shehongbing

Add ability to set library path via COMPLEASM_LIBRARY_PATH if --library_path unspecified

1

Adds the ability to specify the library path (what is set via `--library_path`) using the environment variable `COMPLEASM_LIBRARY_PATH`. The logic is: 1. change default for `--library_path` options wherever they appear...

douglasgscofield

Does compleasm try to download something when run specifying lineage?

10

Hi, I am trying to get compleasm running, but run into an issue. Specifically, I get this error: ``` Traceback (most recent call last): File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 1350, in do_open...

olekto

mammalian database

3

Does Compleasm not support busco's mammalian database? Although I define -l Mammalian, he still downloads and uses 2019 eukaryota,-L also cant use.

sanjin725

Different stats for protein mode

2

Hi, I ran compleasm and BUSCO using protein mode on my annotated genome. Compleasm's result is not good. Is there a change in your hmmsearch or something else? Here are...

arslan9732

compleasm output also cds nucleotide sequences for the final set of genes

3

Hi Thank for this great software. not a bug but a question/enhancement request: Is there a way to also output the coding sequence for each final BUSCO gene? This would...

estolle

compress hmmer output

1

Hi! Thanks for the amazing tool! I was wondering, is it possible for you to add an option `--tar` such as BUSCO has for compressing the hmmer output into a...

dirkjanvw