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Old 05-03-2011, 03:40 AM   #1
Senior Member
Location: uk

Join Date: Jan 2010
Posts: 110
Default Quality control of genomic resequencing data from a HiSeq

Hi all,

We will soon be outsourcing some targeted genomic resequencing on the HiSeq.

I am just wondering, beyond the onboard qulaity value generation and filtration performed by the service provider, what other quality checks should be perfrom subsequently ourselves?

Any input would be appreciated.
gavin.oliver is offline   Reply With Quote
Old 03-05-2013, 07:59 AM   #2
Location: Canada

Join Date: Sep 2012
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I would suggest using a program known as FASTQC, which gives you a lot of summary metrics for read quality, GC content, duplication levels, overrepresented sequences. It's fast and provides very nice graphs for troubleshooting.
chongm is offline   Reply With Quote
Old 06-30-2013, 01:48 AM   #3
Location: india

Join Date: Jun 2013
Posts: 42

Hi chongm,

I have genome of human lymphocytes done on illumina hiseq2000 paired end 2X100bp,
I had done FASTQC and trimmed low quality bases by FASTX tool kit.

I am really struck to go further, kindly explain in detail clarity about indexing human reference genome hg19.

Thank you,
vishnuamaram is offline   Reply With Quote

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