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Old 06-28-2013, 11:33 AM   #1
NGS_New_User
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Default help using velvet for de novo assembly

Hi everyone, i'm trying to run de novo assembly using velvet on short (100bp long) paired end reads.
I first ran velveth and it created only two files named: Log and Sequences.
It also gave me this error:
velveth: Can't malloc 121 chars: Cannot allocate memory

I tried to run velvetg but then I got an error:
[0.000000] No Roadmap file to build upon! Please run velveth (see manual)

This is what I ran using velveth:
$ velveth output_assem 35 -shortPaired -fasta file_PE-1.fa file_PE-2.fa

The two fasta files are already in paired
What does this mean? This is my first time using velvet, and I will appreciate anyone's help. Thanks a lot in advance
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Old 06-28-2013, 04:01 PM   #2
swbarnes2
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I think velvet wants the fastqs to be interleaved. It least older versions did, and they used to include a little perl script that would do that,
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Old 06-28-2013, 06:48 PM   #3
kmcarr
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Quote:
Originally Posted by swbarnes2 View Post
I think velvet wants the fastqs to be interleaved. It least older versions did, and they used to include a little perl script that would do that,
Currrent versions of velvet accept interleaved or separate input files for paired end reads. The default is interleaved; if you are using separate files you have to add the '-separate' option. For your example this would be:
Code:
$ velveth output_assem 35 -shortPaired -fasta -separate file_PE-1.fa file_PE-2.fa
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Old 07-03-2013, 09:44 PM   #4
NGS_New_User
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Thanks for the suggestions! I do appreciate them! I am going to try them, hopefully no errors will pop up
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Old 03-09-2015, 03:30 AM   #5
madhavi
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Hii can anyone help me to run velvet with higher hash value rather than 31 and also how to run velvet optimiser? (illumina short paied end reads)
thanks in advance
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Old 03-09-2015, 03:48 AM   #6
mastal
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to use kmer sizes greater than 31, you need to recompile velvet with

'make ’MAXKMERLENGTH= ’, and put in the max value that you want to be able to use.

See the velvet manual
https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
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Old 03-10-2015, 11:07 PM   #7
madhavi
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Hello mastal
first of all thanks for ur reply.
i have tried this too but it is showing an error as 'compilation terminated.make: *** [obj/readSet.o] Error 1'
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