Reference as input to velvet is giving smaller contig length than without reference.

[azrasid]

HI , I am trying to get a big node length (contig) from the velvet assembly. For that I used reference and Fastq as input to it.

velveth out 31 -reference cyp2c19ref.fa -fastq -shortPaired -separate cyp2c19/NA12878_R1.fq NA12878_R2.fq

and then I used Velvetg

velvetg out_data_78 -exp_cov auto -cov_cutoff auto.

I was expecting some big node length contig but I got small length node contigs( smaller than that I was getting when I didn't use the reference). I wonder why the length of contigs are larger with pure denovo assembly than with reference when given as input.

Am I doing right steps? Please help me with this.

Regards, Azra

[dzerbino]

Hello @azrasid ,

The directories used with velveth and velvetg do not match. Is that normal?

Cheers,

Daniel

[azrasid]

Sorry. I pasted the wrong command. Actually they are matching velvetg out -exp_cov auto -cov_cutoff auto.

[dzerbino]

Hello Azra,

It's hard to diagnose remotely, but this looks correct, as far as I can see.

Have you tried mapping your sequences to the reference, and providing them as a BAM file? The alignments can then be used by Velvet.

It's been a while, so I don't remember what happens to unmapped read in FastQ files.

Cheers,

Daniel

[azrasid]

You suggesting me to map Fastq sequences to the reference and get a Bam file. And then use this BAM file as an input to the Velvet? Really appreciate your response.

[dzerbino]

Yes, exactly.

[azrasid]

Thanks.