show Abstracthide AbstractPteropus giganteus, also known as P. medius and commonly called Indian flying fox, is a frugivorous giant bat, widely distributed in Southeast Asia. Similarly to the other bat species it is endowed with the long life span and the ability to fly at large distances. In addition, it was shown to host numerous viral species including Nipah virus, highly pathogenic for humans, and thus capturing the attention of both scientific and public health communities. The genome of P. giganteus was sequenced using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. The P. giganteus genome, assembled by this method, has a length of 1,985Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19Mb.