You can use SSPACE-LongRead, downloadable from this link: https://www.baseclear.com/services/bioinformatics/basetools/sspace-longread/

Infact authors declare that "Using the long read information, contigs (or scaffolds) are placed in the right order and orientation in so-called super-scaffolds.".

Regards

Thanks, but from the manual, SSPACE-LongRead works with PacBio reads.

SSPACE-LongRead is not restricted to PacBio long reads. It can be used using all long reads technologies, i.e. in the paper below authors reported "Scaffolding

The SSPACE-LongRead perl script was used to scaffold contigs with MinION data."

Link: https://www.nature.com/articles/srep11996#Sec9

Regards