Question: Getting reads contributing to a velvet assembly - contig
0
gravatar for damayanthikherath
22 months ago by
damayanthikherath0 wrote:

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

mapping assembly • 742 views
ADD COMMENTlink modified 22 months ago by lexnederbragt1.2k • written 22 months ago by damayanthikherath0

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.

ADD REPLYlink written 22 months ago by Sej Modha3.8k
1
gravatar for lexnederbragt
22 months ago by
lexnederbragt1.2k
Oslo, Norway
lexnederbragt1.2k wrote:

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.

ADD COMMENTlink written 22 months ago by lexnederbragt1.2k
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