How To Pick The Optimal Parameters For The Velvet Assembler

Question

[nbvasani]

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!

Answer 1

[Dan D]

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.

Answer 2

[Istvan Albert]

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

[nbvasani]

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

[Istvan Albert]

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

[nbvasani]

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

[Istvan Albert]

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

[nbvasani]

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!

Answer 3

[Jeremy Leipzig]

SVAR

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