Getting reads contributing to a velvet assembly - contig
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
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lexnederbragt
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damayanthikherath •
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damayanthikherath •
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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.
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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.