BUSCO : how to download and run with R ?

Question

[Zribz]

Hi all,

I want to do a busco analysis to compare the completeness of 2 versions of Picea glauca transcriptome we de novo assembled. My supervisor tell me I can use R to do this analysis to following this instructions : https://bioconductor.org/packages/release/bioc/vignettes/cogeqc/inst/doc/vignette_01_assessing_genome_assembly.html

I'm beginner in bioinformatics and I don'y understand how to install busco and use it with a R session. In the current bioconductor links we can read : "You must have BUSCO installed and in your PATH to use run_busco(). You can check if BUSCO is installed by running busco_is_installed(). If you don’t have it already, you can manually install it or use a conda virtual environment with the Bioconductor package Herper (Paul, Carroll, and Barrows 2021)." 1- I can't find any information to manually install it with R.. It is faisible ? 2- I tried to use a conda environment but I failed (i.e : Herper package doesn't work any more..).

Anyone know a step by step information to download it and run it by using R ? Or have any usefull informations to help me ?

Thanks a lot for helping !

Answer 1

[Mensur Dlakic]

It is not difficult to google "BUSCO install" and find readily available information about all aspects of the program, including its installation:

https://busco.ezlab.org/busco_userguide.html

BUSCO runs under python and that's how most users will do it. Running it from an R session seems to be possible, but that is more for people who are comfortable with R and don't want to bother with python. It seems to me that either R or python would work for you, and there are detailed instructions at their web sites how to asses genome completeness using native python installation of BUSCO.