Ngs-Qc & K-Mer

Question

[williamjohn360]

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, genome size estimation 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)

[Adrian Pelin]

may i recommend kmergenie for your kmer analysis? it allows selection of multiple kmers and it picks the best one for assemblies.

Answer 1

[jackuser1979]

Take a look at this tutorial for your analysis.