Ngs-Qc & K-Mer

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)

qualitycontrol

• 3,852 views • link

updated 12.5 years ago by jackuser1979

• written 12.5 years ago by williamjohn360

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

• 287 views • link

written 12.5 years ago by Adrian Pelin

1 answer

Take a look at this tutorial for your analysis.

• 0 views • link

written 12.5 years ago by jackuser1979

More posts like this

The soapdenovo2 genome assembly is highly fragmented - learning genome assembly with public data
written 1.4 years ago by JieQY •

I used soapdenovo2 to assemble plant genomes, and the input was a fastq file. But the output failed because N50 was very short, indicating fragmented …
Genome Size Estimation with Jellyfish and Genome Scope is Unexpectedly Small
written 4.7 years ago by dk0319 •

I used jellyfish to count kmers and the obtained histograms were analyzed using Genome scope (http://qb.cshl.edu/genomescope/) in order to estimate effective genome size. However the …
Galaxy workflow concatenate
written 5.8 years ago by avelarbio46 •

Hello everyone! I'm trying to work with workflows on galaxy. I have tested all the tools that I need separetely to confirm that it works, …
Jellyfish: every other kmer count is zero
written 8.2 years ago by Lina F

Hi all, I found a tutorial suggesting how to use Jellyfish to estimate genome size: http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html However, after running `jellyfish count` and `jellyfish histo` the …
K-mer content failed at the beginning of reads
written 9.3 years ago by User 4014 •

Hi, I received data for genome assembly. After using BBduk to trim adapters and low quality reads (Q25), I used FASTQC to check the data, …
Quake Error Corrector
written 10.2 years ago by Seigfried

Hello I have been trying to run Quake Error Corrector on my Illumina reads before assembly. I am following the manual at [http://www.cbcb.umd.edu/software/quake/manual.html][1]. I have …
I Did Not Get Output File When I Ran Fastx_Toolkit
written 13.2 years ago by Raghav

hello you all, I have query regarding quality check of fastq file. I have fastq file of paired end reads generated by illumina sequencing. I …
What Figure You Make For Qc Of Whole Exome Sequencing Data
written 13.3 years ago by User 1933 •

For analyzing QC of fastq files I know fastQC; It generates lots of statistics; Also, there are a set of tools (GATK, <a href='http://samtools.sourceforge.net/'>samtools</a>, <a …
Best Fastq Quality Overview Tool
written 13.8 years ago by William

What is the best tool to get an overview of the quality of your produced reads (in a fastq file)? FastQc <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a> is …
How To Count K-Mer For Color-Space Reads?
written 14.2 years ago by GAO Yang

Hi,guys my former question was here <a href='http://www.biostars.org/post/show/45025/how-to-estimate-genome-size-using-k-mer-coverage/#45148'>http://www.biostars.org/post/show/45025/how-to-estimate-genome-size-using-k-mer-coverage/#45148</a> my problem is this jellyfish could only handle with fasta format files. But mine was color space …