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
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).