Entering edit mode
10.3 years ago
williamjohn360
▴
90
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)
may i recommend kmergenie for your kmer analysis? it allows selection of multiple kmers and it picks the best one for assemblies.