Question: Scafolding and gap filling
0
gravatar for bhagyathimmappa
2.5 years ago by
bhagyathimmappa10 wrote:

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

ADD COMMENTlink modified 2.5 years ago by Sej Modha4.6k • written 2.5 years ago by bhagyathimmappa10

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

ADD REPLYlink written 2.5 years ago by lakhujanivijay4.8k
0
gravatar for bhagyathimmappa
2.5 years ago by
bhagyathimmappa10 wrote:

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.

ADD COMMENTlink written 2.5 years ago by bhagyathimmappa10
0
gravatar for Sej Modha
2.5 years ago by
Sej Modha4.6k
Glasgow, UK
Sej Modha4.6k wrote:

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.

ADD COMMENTlink written 2.5 years ago by Sej Modha4.6k

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?

ADD REPLYlink written 2.5 years ago by bhagyathimmappa10

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

ADD REPLYlink written 2.5 years ago by cmdcolin1.3k
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