Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
How I find not assembly read in a reference assembly??? matiasfreired Bioinformatics 1 04-05-2012 12:13 PM
Genomic comparison Kalily101 Bioinformatics 11 10-12-2011 11:48 AM
Cufflinks and Comparison Analysis DrD2009 Bioinformatics 0 03-10-2010 12:40 PM
Region Comparison DrD2009 Bioinformatics 2 01-29-2010 12:08 PM
Cost comparison jchandler General 0 06-25-2008 09:39 AM

Thread Tools
Old 07-12-2011, 05:42 AM   #1
Location: Belgium

Join Date: Nov 2008
Posts: 79
Default Assembly Comparison

Dear all,

Let's say I have performed several assemblies on the same dataset and I would like to compare the results. I know I can look at N50, average contig length, etc. But I was more thinking of comparing the obtained contigs: how much contigs are the same, how much contigs of assembly1 are imbedded in contigs from assembly2, ...

Thanks for the feedback,

strob is offline   Reply With Quote
Old 07-12-2011, 07:10 AM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 835

you can use minimus2 (or possibly minimus2BLAT) to compare / combine two different assemblies:

for looking at how the assemblies are merged, you can use hawkeye or the listReadPlacedStatus command-line script (these are all part of AMOS). Here's the documentation for the listReadPlacedStatus command:

listReadPlacedStatus [options] -b <bank path>

Prints the status and containing contig(s) of each read as:
iid eid code numcontigs contig iid list

Codes are:
S: Singleton read
P: Placed in a single contig
D: Placed in multiple contigs

-h Display help information
-s Disregard bank locks and write permissions (spy mode)
-v Display the compatible bank version

-S Just list singleton reads
-D Just list duplicate reads
-P Just list placed reads

-E Just list read EIDs
-I Just list read IIDs

amos bank, reads
gringer 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 12:44 AM.

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