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The recent advances in high throughput sequencing methods have led to a drastic increase in the number of released draft genome sequences. However, the completion of these newly sequenced draft genomes greatly varies and their quality remains an important challenge. Because assembly quality highly impacts subsequent exploitation of reference sequences, we implemented a semi-automated protocol to improve a reference sequence. We propose a modular approach that can use deep coverage of long insert-size paired-reads or genotyping by sequencing (GBS) of segregating populations, or Optical mapping data. As a proof of concept, this approach has been used to produce a new version of the banana (Musa acuminata) reference genome sequence that was greatly improved. |