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Old 05-15-2019, 04:30 AM   #1
obriht
Junior Member
 
Location: France

Join Date: May 2019
Posts: 3
Default SOAPdeNovo, get the contigs

Hello all,
I am writing this message because I will need help with SOAPDeNovo. Indeed, I made an assembly of Novo with this tool and I want to recover the final contigs. I'm outputting two files. The first file in .contig corresponding to contig sequences without using mate pair information . The second file is in .ScafSeq containing scaffold sequences.
On the SOAP website , it is specified that the final contigs can be extracted by decomposing the scaffold sequences at the level of the gap regions.
I would like to know how to achieve this decomposition in order to get the contigs?
Hoping that you could help me I wish you a great day.
Cordially
(Sorry for my bad level in english)
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Old 05-21-2019, 05:55 AM   #2
colindaven
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Location: Germany

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Why not use the scaffolds ? These are the final contigs organised into scaffolds by using the supplied probably mate pair info. This is what I have always used.

If you still want the contigs, maybe just break the scaffolds at long N stretches ?

If its an illumina assembly, it is likely to be pretty awful. Long reads are the way to go these days as I'm sure you know.
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Old 05-23-2019, 04:59 AM   #3
obriht
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Hello, I want to thank you for your answer.
I wanted to recover contigs because I want to scaffolding from two files containing separate contigs.
Thank you very much for your response and your help
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