Fig. 1

A workflow of the PhaseDancer algorithm and the accompanying tools. PhaseDancer works with next generation sequencing long-read data e.g. Oxford Nanopore or PacBio. Starting with an initial anchor sequence, the core workflow of PhaseDancer iterates along four major steps: (i) mapping the reads on the anchor sequence, (ii) clustering the mapped reads and selection of a cluster with the reads originating from the genomic region represented by the anchor sequence, (iii) assembling these reads into a contig, and (iv) extending the current anchor sequence using the contig to a new anchor sequence processed in the next iteration. After all iterations, the algorithm outputs the final assembled sequence. PhaseDancer is also accompanied with two supporting tools - the semi-supervised character of PhaseDancer is complemented by PhaseDancerViewer that enables the intermediate control of assembly process, whereas PhaseDancerSimulator generates in silico data for profound validation of the algorithm. Thanks to its high efficiency, PhaseDancer can be used for resolving challenging genomic tasks, involving segmental duplication (SD) assembly