Question: Post Assembly Gap Filling
2
gravatar for HG
5.9 years ago by
HG1.1k
Germany
HG1.1k wrote:

Hi every one i am doing some plamid genome assembly with spades. After assembly i used SSPACE for scaffolding. But there are some gap each of the draft genome. I can fill the gap by PCR. But i want to reduce the number of gap insilico?? Can anyone suggest how to reduce the gap ?? If i do mapping the reads with contigs will it be give any promising result???

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ADD COMMENTlink modified 5.9 years ago by martenboetzer2130 • written 5.9 years ago by HG1.1k
1

I used finishing scripts for my work on sequencing of mitochondrial genome. Hope this will be useful for you as well. http://www.cbcb.umd.edu/finishing/

ADD REPLYlink written 5.9 years ago by RT340
8
gravatar for martenboetzer2
5.9 years ago by
martenboetzer2130 wrote:

There are a few in silico tools that can fill in the gaps within scaffolds;

GapFiller (developed by myself, I'm also the developer of SSPACE): http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/ http://genomebiology.com/2012/13/6/R56

IMAGE2: http://sourceforge.net/apps/mediawiki/image2/index.php?title=Main_Page

GapCloser (part of SOAP): http://sourceforge.net/projects/soapdenovo2/files/GapCloser/

Regards, Boetsie

ADD COMMENTlink written 5.9 years ago by martenboetzer2130

Dear Boetsie

I've tried all three of the above programs, for GapCloser and IMAGE, report files indicated that no gaps are filled and Gap filler hangs then crashes on the first iteration. My assembly is Eukarytic, built with SPAdes, using PE and Minion reads. I am doing the gap closing with same PE reads used to assemble the genome. Is this why gap closing is failing? Are we supposed to use a different read library for the gap closing?

Thanks and kind regards Crystal

ADD REPLYlink written 11 months ago by larvalanobium20
1
gravatar for Biojl
5.9 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

If you use paired reads you can take a look to: GapFiller

I haven't test it myself, though.

ADD COMMENTlink written 5.9 years ago by Biojl1.7k
1
gravatar for Leszek
5.9 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

GapCloser from SOAPdenono works perfect for me.
To use it, you will need paired-end or mate-pair reads.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Leszek4.0k

To run GapCloser from SOAP denovo , is it necessary to assemble with Soap denovo?? or else i can use different assembler. After that i can upload reads and contig ??? Currently i am using Spades 2.5.1

ADD REPLYlink written 5.9 years ago by HG1.1k

no, as described in the program manual, you need assembly in fasta, reads in fastq or fasta and config file

ADD REPLYlink written 5.9 years ago by Leszek4.0k
0
gravatar for Adrian Pelin
5.9 years ago by
Adrian Pelin2.3k
Canada
Adrian Pelin2.3k wrote:

Your genome is circular, correct?

Your current assembly resulted in the entire genome as a scaffold with gaps (NNNs), but otherwise, your scaffold is circular, correct?

You can try iterative read mapping. You can do that either with CONSED (free) or Geneious (14 day free trial). When you map iteratively, each time an iteration is complete, the idea is that your contigs will be extended slightly. At one point, they should overlap. The bigger the read lengths, the faster you will be done.

ADD COMMENTlink written 5.9 years ago by Adrian Pelin2.3k

This is IMAGE2's strategy. See martenboetzer2's (Boetsie's) answer.

ADD REPLYlink written 5.9 years ago by Lee Katz2.9k
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