Question: How to run velvetoptimiser on paired-end FASTQ datasets
gravatar for whatup
3.8 years ago by
United States
whatup30 wrote:


Running Velvet has always been confusing for me.  So, I have always been running it using VelvetOptimiser in order to avoid dealing with searching for optimal parameter values.

If I run VelvetOptimiser to assembled a set of paired_end FASTQ sequences, then does this mean I do not need to run Velveth and Velvetg at all? (I am asking this because I am not so satisfied with the result.  Most of the contigs from running only VelvetOptimiser seem too short)


Here is the basic steps that I take to VelvetOptimiser.

1) I convert two FASTQ files into one using '' since Velvet requires that paired-end FASTA and FASTQ datasets come in a single merged file.

2) then I run velvetoptimiser as following: -s 27 -e 31 -t 8 -d '/outputfolder' -f '-fastq -shortPaired theMergedFile.fastq'    


#2 run without any error.  However, the resulted contig length are too short.  I know they are too short because I ran it also using Trinity assembly.  Maybe it's the default parameter values '-s 27 -e 31' that is causing this problem. Can you spot what I might be doing wrong?


ADD COMMENTlink modified 3.8 years ago by Philipp Bayer5.5k • written 3.8 years ago by whatup30
gravatar for Philipp Bayer
3.8 years ago by
Philipp Bayer5.5k
Philipp Bayer5.5k wrote:

It looks like you assemble RNASeq, is that right? You might want to use Oases with your Velvet results, have a look at the paper comparing Oases to Trinity:

It corrects and scaffolds your contigs so you should see longer ones. As far as I know, Velvet was built mostly for genomic contigs, so it assumes a few things that Oases corrects, Trinity was built for RNASeq so it's no wonder you see longer contigs.

For your other questions:

Yes, VelvetOptimiser runs velvetg and velveth internally, so you can use the final results. Which optimal k-mer value does it report? If it reports 31, your range might not be inclusive enough, try something larger for the end value.

ADD COMMENTlink written 3.8 years ago by Philipp Bayer5.5k

Thank you for your advice!  It's already clearing things up for me.  I'll have a look at Oases as you suggested.

ADD REPLYlink written 3.8 years ago by whatup30

yes, it is RNASeq

ADD REPLYlink written 3.8 years ago by whatup30
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