Scafolding and gap filling

Question

[bhagyathimmappa]

Hello all,

for one of the novel fungi, we did illumina mi-seq paired end sequencing and used velvet to assemble, I have 15500 contigs.

some information about reads (after removing adapters and poor quality bases):

Encoding : Sanger / Illumina 1.9

Total Sequences : 1747634

Sequence length : 36-301

If I had extra/additional reads I could have tried scaffolding or gap filling. Is there any option to reduce number of contigs?

Thanks Bhagya C T

[lakhujanivijay]

Can you please provide some information on the "extra/additional reads" ?

Answer 1

[bhagyathimmappa]

I have paired end reads from Mi-seq only, I do not have any other reads. To do scaffolding or gap filling I should have extra reads right?

Whatever the reads I got from Mi-seq paired end sequencing I used for velvet denovo assembly.

Answer 2

[Sej Modha]

For gap filling you can use GapFiller and use reference based scaffolding tool such as Scaffold_builder or reference independent scaffolding tool e.g. SSPACE.

[bhagyathimmappa]

Thank you.

I do not have any additional reads to use for scaffolding, all I have is illumina Mi-seq paired end data. I still just tried to use SSPACE with denovo assembled genome file and paired end data(same ones, used for denovo assembly). It resulted in exact same number of contigs observed in the denovo assembled file.

It looks like if I do not have any additional reads, I cannot do anything further to improve the assembly?

[cmdcolin]

You can possibly use a "reference based scaffolder" such as medusa, ragout, or other tools. This compares a genome to a closely related one and uses synteny to infer scaffolding