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Old 08-13-2019, 03:27 PM   #1
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Location: USA

Join Date: Aug 2019
Posts: 5
Default de novo assembly using Velvet to reconstruct a PCR amplicon

Hi all. I'm a newbie in de novo assembly. I have successfully installed Velvet, was able to get it to read my fastq and run of my test set, but it is not giving me the expected result.

This sample came from a 100% clonal PCR amplicon that is ~9000bp in length. The amplicon is tagmented using Nextera XT, and put into Illumina MiSeq (multiplexed run of 96 samples). My fastq contains MiSeq non-pair-end reads with length 142bp. After de novo assembly, I am hoping to get one single contig that constructs the original 9000bp PCR amplicon. But for whatever result I am unable to get Velvet to produce contigs over like 500bp.

Please see an example of my command below

$ ./velveth ./assembly 21 -fastq S4411.fastq
$ ./velvetg ./assembly

This gave me 629 tiny contigs <500bp. There should only be one contig, and the software Geneious was able to produce that 1 contig.
Any pointers how to work with Velvet?

You can download the fastq file here.

Thank you so much in advance.
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