Question: SPAdes assembly and scaffold generation
gravatar for nkvnambiar
5.0 years ago by
nkvnambiar0 wrote:

Hi Sir/Madam,


Myself Nithya, currently working as a Bioinformatics Programmer at Scigenom labs, Cochin, Kerala,India.I am very new to the field of next generation sequencing.  I have got some doubts regarding the output generated by SPAdes. Hope you can help me in this regard. The questions are as follows:


1.  Did the assembly program combine the sequences into scaffolds using runs of N's to represent gaps between ordered and oriented contiguous sequences?

2. Does every N in the scaffold represents a gap? Alternatively, does the sequence include single or short runs of N's that represent ambiguous base calls? 


Waiting forward for your reply.

Thank You

next-gen assembly • 2.8k views
ADD COMMENTlink modified 17 months ago by cruiz_perez0 • written 5.0 years ago by nkvnambiar0
gravatar for cruiz_perez
17 months ago by
cruiz_perez0 wrote:

Hi Nithya! For what I understand from SPAdes output, you have one file which contains the contigs and should not contain any Ns. On the other hand, you have a scaffolds fasta file, in which the program attempted to join contigs based on read pairs and based on the assembly graph. You can find more information in the manual: For your second question, I believe if you do quality trimming of your reads before assembly it is highly unlikely you are going to end up with reads with long stretches of N so probably those you see are gaps joining contigs.


ADD COMMENTlink written 17 months ago by cruiz_perez0
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