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Production of high quality reference genome sequences for non-model organisms remains a challenging undertaking, especially for large (>1 Gbp) genomes. For such projects, de novo whole-genome assembly typically requires billions of sequencing reads from several different types of DNA libraries. An attractive alternative for generating reference sequences can be achieved through targeted assembly of gene/transcript sequences of interest. Even for species with scant transcriptomic sequence information, there are likely existing sequences that could be used to aid de novo assembly, such as homologous gene sequences from a related organism.
(Kucuk et al., 2017) Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics.