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 'shuffleSequences_fastq.pl' since Velvet requires that paired-end FASTA and FASTQ datasets come in a single merged file.
2) then I run velvetoptimiser as following:
VelvetOptimiser.pl -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?