Question: Assembly of wheat genome
gravatar for mustafa_aljadi
19 months ago by
mustafa_aljadi0 wrote:

Dear All I just start working on the assembly of wheat with out a genome reference. My question which is the best assembly programs that are commonly used in recent two years 2016-2017? I did some researches and found out just one called Falcon Thanks Mustafa

assembly • 549 views
ADD COMMENTlink modified 19 months ago by Michael Dondrup45k • written 19 months ago by mustafa_aljadi0

Not to sound pessimistic but you do realize that de novo assembly of wheat genome is a difficult computational task because of the size/ploidy. What kind of sequence data do you have and how much? Do you have access to significant hardware resources to try this?

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax63k

Which kind of reads will you have? Illumina, PacBio or mixed?

ADD REPLYlink written 19 months ago by Fabio Marroni2.1k
gravatar for Michael Dondrup
19 months ago by
Bergen, Norway
Michael Dondrup45k wrote:

Short answer: Abyss assembler was used in the wheat genome paper.

See the supplementary materials section:

Quality filtered reads were de novo assembled using ABySS ... Seven additional diploid and tetraploid wheat genomes were shotgun sequenced and Illumina PE short reads de novo assembled using the CLC assembler.

Anyway, you maybe do not want to choose a project of that size - a 17-gigabase hexaploid, polymorphic and highly repetitive genome - as a beginner. There is a reason for that the paper has around 80 authors (though the assembly might be a smaller part).

ADD COMMENTlink written 19 months ago by Michael Dondrup45k
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