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Old 07-12-2011, 05:42 AM   #1
strob
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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,

Steven
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Old 07-12-2011, 07:10 AM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838
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you can use minimus2 (or possibly minimus2BLAT) to compare / combine two different assemblies:
https://sourceforge.net/apps/mediawi...title=Minimus2

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:

.USAGE.
listReadPlacedStatus [options] -b <bank path>

.DESCRIPTION.
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

.OPTIONS.
-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

.KEYWORDS.
amos bank, reads
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