How to generate AGP format using contigs and scaffolds

Question

[Prakki Rama]

Hi all,

The scaffolds I work on were generated using transcriptome data by L_RNA_Scaffolder. But, I want to know how the scaffolding was done by generating an AGP output (helpful in NCBI submission too). We can try to aligning the contigs on to the scaffolds but my worry is, there is chance of error creeping in. Thanks in advance.

Answer 1

[####]

This might help you.

It is a perl program , just run the code and you will get three output file .agp scaffold.fasta, contigs.fasta

Hope this will help

[Prakki Rama]

Thank you very much. Already found a script from velvet software.