SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Estimating the bacterial genome size using Kmer frequency Krish_143 Bioinformatics 3 06-02-2013 02:13 PM
Help with finding complementary sequences in ngs data Ami Bioinformatics 1 04-02-2013 11:48 PM
Relationship between kmer size and read length and total no.of reads. ? vaibhavvsk Introductions 2 03-19-2013 06:25 AM
estimate genome size through kmer analysis plantae Bioinformatics 0 07-05-2012 03:46 AM
estimate genome size through kmer analysis plantae De novo discovery 0 07-05-2012 03:36 AM

Reply
 
Thread Tools
Old 01-23-2014, 09:47 PM   #1
bioman1
Member
 
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
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

This workflow/tools are quite good.
TiborNagy is offline   Reply With Quote
Reply

Tags
k-mer, qualitycheck

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:57 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO