how to use bambus for scaffolding?

[elisadouzi]

How to make mates file from the velvet contig output for bambus. The IID of velvet contig file(convert by amos package) is always the numbers, how can we tell the paired-end sequence from this file?

Thanks!

[rahularjun86]

How to make mates file from the velvet contig output for bambus. The IID of velvet contig file(convert by amos package) is always the numbers, how can we tell the paired-end sequence from this file?

Thanks!

Hi,
I am also trying to do the same. Have you already generated the bambus2 required input files(.contig and .mate)? I have .contig file from the minimus2 run, But I am not sure how to get .mate file. Can I generate it from the Illumina paired-end reads information? the reads I assembled??
Best regards,
Rahul

[dan]

I gave up on bambus after wrestling with the docs for months. The paper makes it sound great, but I couldn't get it working.

[yifangt]

Same here!
Bambus2 within AMOS did not work for me either. Is it possible to open an a thread in this forum?