Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
CANU-correct subreads individually VS batch lguzmanz Pacific Biosciences 2 06-08-2016 09:38 AM
Keep quality score when correcting with Canu assembler? lguzmanz Pacific Biosciences 1 04-21-2016 09:57 AM
Canu error: 'failed to create the overlap store' lguzmanz Pacific Biosciences 0 04-20-2016 03:54 PM
TopHat Fusion: -r parameter sensitivity Khaz RNA Sequencing 0 06-11-2012 07:49 AM
calculation of sensitivity and specificity happy2000 Bioinformatics 3 06-10-2011 06:26 AM

Thread Tools
Old 09-28-2016, 10:01 AM   #1
Location: Fayetteville, AR

Join Date: Apr 2014
Posts: 85
Default Canu sensitivity to genomeSize parameter

I am currently working with some Bio faculty on a de novo assembly of Centruroides vittatus (Striped Bark Scorpion). One difficulty I seem to be having involves the command line parameter "genomeSize=" in Canu. Of course, one of the real difficulties with de novo is you likely don't know the size of the genome. You may not even have an estimate from a close relative species.

I currently have two PacBio runs (different specimens in each) labeled Q1133 and Q1171. It seems that by varying the "genomeSize=" parameter, the output of the assembly can be significantly different! I am attaching a Quast output for some recent runs...two for each data set, with only the genomeSize parameter modified (genomeSize=170 and genomeSize=350).

It seems that not many people have produced tools to estimate genome size in new projects that involve PacBio or ONT data...I did have some old Illumina data that was kind of iffy, but I tried the new GenomeScope tool from Schatz, et al and it comes up pretty consistently around 180Mb for an expected genome size. It was suggested to try the tool using the corrected reads out of Canu, but the tool doesn't seem to be able to evaluate that sort of input at this time.

Any suggestions on how to best approach the problem (if it IS a problem and not simply an error on my part)? I am using essentially default values in Canu.
Attached Files
File Type: pdf report.pdf (47.1 KB, 6 views)
jpummil is offline   Reply With Quote
Old 09-28-2016, 03:31 PM   #2
Senior Member
Location: San Francisco

Join Date: Aug 2012
Posts: 322

Now that you have some contigs, why not map all your raw data to one of the assemblies and look at the coverage distribution across the contigs.
rhall is offline   Reply With Quote

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 06:53 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO