Question: Is There A Tutorial/Guide Explaining How To Create A Draft Genome From Assembled Contigs?
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gravatar for Arpitha Hebbar
5.4 years ago by
India
Arpitha Hebbar170 wrote:

hello

I have a contigs. (reads are generated from Ion-Torrent PGM) i have to create a draft genome from the contigs.

Which software will be help full ? i have no idea about this.

Please can u help....

ngs contigs ion-torrent • 3.3k views
ADD COMMENTlink modified 5.4 years ago by Josh Herr5.6k • written 5.4 years ago by Arpitha Hebbar170

Do you mean, how to assembly your contigs? What organism is it?

ADD REPLYlink written 5.4 years ago by Björn650

yes exactly. how to assemble the contigs. m working on Staph aureus.

ADD REPLYlink written 5.4 years ago by Arpitha Hebbar170
1
gravatar for Josh Herr
5.4 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

This is not as straightforward as you might think and the process of moving from contigs to a draft genome is difficult. This can vary on the type of organism, the size of the genome, the frequency of gene space, the depth of sequencing, etc. You didn't give us any of this information so it's hard to guide you. There are numerous ways to close contigs or scaffolds but much of this depends on how similar your sequenced contigs are to those from already sequenced genomes.

If you have a relatively small genome (bacterial or very small eukaryote less than ~40Mb), I have had good luck using the PAGIT pipeline (Post Assembly Genome Improvement Tool) (see these links for the pipeline and paper). This pipeline (as well as others like this) require a lot of memory, so you won't be able to do this on a laptop or desktop computer.

ADD COMMENTlink written 5.4 years ago by Josh Herr5.6k

hey thnx ... m working on a bacterial genome S.aureus. m using de novo method. actually i tried PAGIT. but while running the image.pl it is showing the error cant execute fasta2singleLine.pl. i used the input file which is generated from the abacas. i tried both with .fasta file as well as .contigsinbin.fasta. pls help me in this....

ADD REPLYlink written 5.4 years ago by Arpitha Hebbar170
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