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Old 01-23-2014, 09:47 PM   #1
Location: US

Join Date: May 2012
Posts: 80
Default NGS data-QC, Kmer, Genome size finding

I am new to NGS, I have just received sequenced raw files of non-model plant from Hiseq. I would like to know sequence quality check for quality filtering. I also like to do K-mer analysis and heterozygosity rate analysis. Please let me know the best tools to do this.

I have selected these workflow/tools, better workflow/tool recommendation are welcome.
raw reads->Sequence quality check - FastQC->K-mer analysis- Jellyfish ->to estimate genome size & Heterozygosity rate analysis- GCE (genomic charactor estimator)
bioman1 is offline   Reply With Quote
Old 01-24-2014, 03:23 AM   #2
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Location: Budapest

Join Date: Mar 2010
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This workflow/tools are quite good.
TiborNagy is offline   Reply With Quote

k-mer, qualitycheck

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