The completion of a chromosome-scale reference sequence for bread wheat cultivar Chinese Spring marks a milestone for wheat genomics. A possible direction for future research in wheat genomics is the assembly of genome sequence for representatives of global wheat diversity. An important component in this endeavour will be a reproducible, open-source pipeline for sequence assembly, enabling fast and cost-effective assembly of a large number of genotypes. In this presentation, I will introduce a computational workflow to construct chromosome-scale sequence assemblies in Triticeae species based on a combination paired-end, mate-pair, Chromium 10X and chromosome conformation capture sequencing data. The pipeline was evaluated on the published raw data for the IWGSC Chinese Spring reference assembly and the assembly of wild emmer accession Zavitan. Moreover, first results on a reference genome sequence assemblies for a diploid wild relatives of wheat will be presented. The implications for wheat pan-genomics and genetic analyses in wheat wild relatives will be discussed. The software is available at https://triticeae.bitbucket.io.