Question: Is Gap Closing Mandatory Process For Soapdenovo Assembly?
gravatar for toshnam
8.0 years ago by
Seoul, Republic of Korea
toshnam620 wrote:

Hi all,

I assembled paired-end genome sequences using SOAPdenovo, and got some scaffold sequences.

I found GapCloser program which is designed to close the gaps emerging during the scaffolding process by SOAPdenovo, and ran it against my scaffold sequences.

However I found the GapCloser trimmed 'N' in scaffold sequences only. Should do I remove 'N' sequence in scaffold? Is it mandatory step?

Thanks for your comment in advance.

ADD COMMENTlink modified 8.0 years ago by Benm710 • written 8.0 years ago by toshnam620
gravatar for Benm
8.0 years ago by
Benm710 wrote:

Gapcloser is use the PE/MP reads to re-map to the scaffolds, if one end of PE/MP is mapped to the sequence(not 'N'), and the other is mapped to the gaps(Ns reads), it will use the gap' s mapping reads to construct the gap's sequence, that named 'GapCloser' process. So you can remove 'N' sequence from the scaffolds.

ADD COMMENTlink written 8.0 years ago by Benm710

Are you saying GapCloser is mandatory process for PE read because PE assembly can include gap sequence?

ADD REPLYlink written 8.0 years ago by toshnam620

Because most of gaps should be repeat or non/low sequenced regions, it may be in higher coverage depth or lower, if it is repeat, it will generate too many bubbles, or if it is lower coverage, it also can't be effectively to build contigs by not enough kmers, so sequence in gaps can't be constructed based on de Brujin graph algorithm. GapCloser is a amendatory tool, which allowed low confidence reads to mapped reads to the 'reference' sequence, and it masks exact repeats identified from the shotgun data, it is similar with the algorithm of "RePS" which also developed by BGI.

ADD REPLYlink written 8.0 years ago by Benm710

Thank you for your kind reply.

ADD REPLYlink written 8.0 years ago by toshnam620
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