high number of contig produced from genome assembly

Dr khani · 12-26-2017, 04:34 AM

i have 11700000 paired end reads.when i run denovo assembly by Genious , 130000 contig is produced. can i help me to in this issue?????

GenoMax · 12-26-2017, 06:22 AM

Your best bet is to contact Geneious tech support. Your question is very generic and you are using a commercial software package which is going to make it difficult to get useful help here.

luc · 12-26-2017, 02:27 PM

Anybody looking at this would need some more info: What type of organism? Which genome size is expected? What read lengths did you use? What library prep protocol and insert sizes?

Gorgon_VZ · 01-03-2018, 02:42 AM

Given the fact that issues can occur anywhere beginning from samplequality,library-preparation, sequencing and last but not least parameter-settings used for assembly, it is hard to provide help with this minimum amount of information. But probably the first, cost and time effective thing you could try is to test a range of different kmer-sizes and keeping track of the changes in N50. Another thing you could check if your genome is diluted by very short sequence clusters (nearly readlength). Maybe throwing away all contigs <200bp still represents 99% of your target genome and you will end up with much less contigs in total.

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12-26-2017, 04:34 AM	#1
Dr khani Junior Member Location: Tehran Join Date: Jan 2017 Posts: 3	high number of contig produced from genome assembly i have 11700000 paired end reads.when i run denovo assembly by Genious , 130000 contig is produced. can i help me to in this issue?????

12-26-2017, 06:22 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,825	Your best bet is to contact Geneious tech support. Your question is very generic and you are using a commercial software package which is going to make it difficult to get useful help here.

12-26-2017, 02:27 PM	#3
luc Senior Member Location: US Join Date: Dec 2010 Posts: 356	Anybody looking at this would need some more info: What type of organism? Which genome size is expected? What read lengths did you use? What library prep protocol and insert sizes?

01-03-2018, 02:42 AM	#4
Gorgon_VZ Member Location: Germany Join Date: Oct 2016 Posts: 10	Given the fact that issues can occur anywhere beginning from samplequality,library-preparation, sequencing and last but not least parameter-settings used for assembly, it is hard to provide help with this minimum amount of information. But probably the first, cost and time effective thing you could try is to test a range of different kmer-sizes and keeping track of the changes in N50. Another thing you could check if your genome is diluted by very short sequence clusters (nearly readlength). Maybe throwing away all contigs <200bp still represents 99% of your target genome and you will end up with much less contigs in total.