ablab
How to generate an agp file from the scaffolds of spades?
Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.
Hello, I have to submit some genomes to ENA (European Nucleotide Archive) and I would like to have an agp file to inform how the contigs were assembled by spades into scaffolds. I there a way to get such file? I am using this version of the tool: spades/3.15.5 . I saw that there is a file called 'scaffolds.paths' which could be usefull.
Describe the solution you'd like
If possible I'd like that the agp generation would be included in the output from spades in the next release
Describe alternatives you've considered
No response
Additional context
No response
Hello
You may use some third-party tools for conversion to these legacy formats. IIRC gfastats was able to do something like this
Hello I tried gfastats but didn't manage to find which command to use to get an agp file so I'll submit only the genome as an .embl file (with annotations).