Question: How To Pick The Optimal Parameters For The Velvet Assembler
6
gravatar for nbvasani
6.3 years ago by
nbvasani230
United States
nbvasani230 wrote:

Hello Everyone,

This is the first time I am using Velveth and velvetg. I have around 5 million read, which has 50-300bp. I used below cmd, and it work jusdt fine.

# velveth auto 31,45,2 -fastq -short -inputfile

output

#  it gave me 7 file with kmer length 31,33,35,36,39,41 &43.

Can anybody please give me suggetion about which kmer length to select, do i need to use long or shord read in command?

How do I excecute velvetg cmd? What cutoff and min_contig_length to use?

Thanks in advance!

velvet • 10k views
ADD COMMENTlink modified 6.2 years ago by Dan D6.9k • written 6.3 years ago by nbvasani230
2
gravatar for Dan D
6.2 years ago by
Dan D6.9k
Tennessee
Dan D6.9k wrote:

This whole article is worth reading, but I'll link to the paragraph of special interest to your question:

http://ged.msu.edu/angus/diginorm-2012/tutorial.html#assembling-with-velvet

The khmer toolset comes with an assemstats3.py script that gives a nice table output of the assembly statistics.

ADD COMMENTlink written 6.2 years ago by Dan D6.9k
1
gravatar for Istvan Albert
6.3 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

Tools that help with these decisions are the Velvet Advisor

http://dna.med.monash.edu.au/~torsten/velvet_advisor/

and the Velvet Optimizer:

http://bioinformatics.net.au/software.velvetoptimiser.shtml

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Istvan Albert ♦♦ 81k

There is no discussion about single end read in manual. So how can I execute velveth cmd. And my fastq file has 50-300bp long single end read. For eg:

# velveth auto 31 -fastq -short -inputfile
or
# velveth auto 31 -fastq -long -inputfile
ADD REPLYlink modified 6.3 years ago by Istvan Albert ♦♦ 81k • written 6.3 years ago by nbvasani230

if you don't explicitly call it with paired option shortPaired then it will operate in single end mode

ADD REPLYlink written 6.3 years ago by Istvan Albert ♦♦ 81k

Thanks Istvan Albert. my fastq file has 50-300bp long single end read. So what do i consider my read as short or long?

ADD REPLYlink written 6.3 years ago by nbvasani230

the answer is above, have you run the Velvet Advisor? it will give you the answer you seek

ADD REPLYlink written 6.3 years ago by Istvan Albert ♦♦ 81k

Yes I have run velvet advisor. But I was confuse as it was not showing read range. But then I selected 50 and 300 seperatly, and it shows same both time velvet sequence type -short. Thanks a lot. I really appriciate your help. Sorry for bothering on same thing. Cheers!

ADD REPLYlink written 6.3 years ago by nbvasani230
1
gravatar for Jeremy Leipzig
6.3 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

SVAR

https://code.google.com/p/standardized-velvet-assembly-report/

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Jeremy Leipzig18k
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