Getting reads contributing to a velvet assembly - contig

Question

[damayanthikherath]

Dear all,

I have a fasta file of contigs generated after assembling the reads using Velvet. Can anyone help me with how to get information on the original read ids , contributing to each of the contig using the outputs from Velvet?

Thank you

[Sej Modha]

I am not sure how to do this using Velvet output but you can always align reads back to the contigs and extract this information from the sam or bam file.

Answer 1

[lexnederbragt]

if you use the -amos_file yes flag for velvetg, you'll get an afg file which contains this information. The viewer Tablet can be used to inspect the results. There may be suitable parsers/converters for the afg file that help you get what you need.