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Old 05-28-2012, 02:20 AM   #1
Junior Member
Location: Spain

Join Date: May 2012
Posts: 10
Default Velvet Question

Hello, i am a new Velvet user and i am trying to assemble some libraries that i found in this site:

I have some question about Velvet:

1) Shuffle operation is needed always when more than 1 library is assembled? If is not needed always in what it helps?

2)I saw this operation in the recipes of the site i mentioned: shortjump_1.fastq shortjump_2.fastq - | fastx_reverse_complement > shortjump.fastq
What - | fastx_reverse_complement > shortjump.fastq is needed for?

3)Using the the command above i have the following error:
/var/spool/slurmd/job414800/slurm_script: line 21: fastx_reverse_complement: command not found
Why this error is produced? Is it a problem of slurm? Can i fix it or there is another alternative?

4) I also tried to use:
fastq -shortPaired frag.fastq -shortPaired2 shortjump.fastq -shortPaired3 longjump.fastq
but i have a problem with -shortPaired3. I have to put at max 2 parameters?

Thank you a lot
VNou is offline   Reply With Quote
Old 05-28-2012, 07:07 AM   #2
Location: Frankfurt(M), Germany

Join Date: Jan 2011
Posts: 58

1). Shuffle script is to convert two paired files to single file readable by velveth. Please go through this link:
2). I have not tried this before, you can refer the fastx tools(, and see the command used, it is for Producing the Reverse-complement of each sequence in a FASTQ/FASTA file.
3). "fastx_reverse_complement: command not found" because you do not have fastx installed on your system. But why do you want to Reverse-complement your sequences ???
4). Your velvet installation is not supporting the 3rd library, Please re-install velvet with >2-3 libraries. And refer the section "2.3.2 CATEGORIES" of velevt manual "". By default, there are only two short read categories, but this variable can be extended to your needs.
Must go through this link:
Best wishes,
Rahul Sharma,
Frankfurt am Main, Germany
rahularjun86 is offline   Reply With Quote
Old 05-28-2012, 07:46 AM   #3
Junior Member
Location: Spain

Join Date: May 2012
Posts: 10

First of all thanks a lot for your answers.
I want to ask something more about the command :
- | fastx_reverse_complement > shortjump.fastq. Instead of installing fastx is there any other way to do it? Why here the use it?
I assembled without using it and just shuffling the 2 short jump libraries but i get in the case of Rhodobacter sphaeroides a N50 of 27bp and i think is too small. The input parameters i used are the same with the site(k-mer 31 exp_cov auto). They obtain i much bigger N50 358kbp. I think the problem is related to the reverse complement. Do you have any idea about what can i do to solve the problem without install fastx tools because i encounter difficulties in installing them?
Thanks again a lot
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