SPAdes assembly and scaffold generation

Question

[nkvnambiar]

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

Answer 1

[Carlos]

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: http://spades.bioinf.spbau.ru/release3.10.1/manual.html.

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.

Cheers!