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Old 10-28-2015, 12:41 AM   #1
angus1024
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Location: cambridge uk

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Default Where is documentation for Velvet software assembly please.

Greetings,

I ask very newbi questions.

I am trying to understand how to use Velvet (parameters and understand the output) and seek documentation, have read the manual (maybe 21 pages) but thats all I can find.

Currently, as a test, I try to assemble about 500bp from a very well defined fastq file and do not understand the velvet output. The relevant file (I understand) is called 'LastGraph' containing about 12 contigs and 18 lines starting with the word 'ARC'. I expected a single contig. I would guess a graph could be constructed with these 12 contigs as Vertices and the 18 ARCs as edges but I cannot see this. Also the contigs are pairs which I imagine are somehow (reverse) complemented - but I also do not see this.

Any comments welcome (especially about LastGraph format/'meaning') and pointers to documentation. I have spent maybe 2 days on this and put in effort and seem to be at a dead end.

Thanks
angus1024
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Old 10-28-2015, 05:30 AM   #2
turnersd
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You might try the protocol. Maybe do a little searching around before posting.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952100/
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Old 10-28-2015, 07:51 AM   #3
angus1024
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Quote:
Originally Posted by turnersd View Post
You might try the protocol. Maybe do a little searching around before posting.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952100/
Thanks TurnerSD, appreciated. I had put in effort and try not to waste peoples time.

I'd already seen this one - will reread it including the references in case I missed something.

I still do not understand the knowledge embedded within the Velvet output file called LastGraph.

Thanks
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Old 10-28-2015, 10:19 AM   #4
Ancestro
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Maybe you might look at this

https://helix.nih.gov/Applications/velvet_manual.pdf

LastGraph explanation Retrieved from the same doc. http://imgur.com/R9TZBWN

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Old 10-28-2015, 01:08 PM   #5
angus1024
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Smile Thank you

Thank you very much indeed Ancestro. Just the info I was after.

But I had read this document and missed the section !!! I really was at a dead end. Apologies for taking up your time and I am grateful.

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