engleski

Rala - Rapid layout module for de novo genome assembly

Rala is a standalone layout module intended for assembly of raw reads generated by third generation sequencing platforms. It consists of two parts, read preprocessing inspired by HINGE (Kamath et al, 2017), and assembly graph simplification as described in Miniasm (Li, 2016). In preprocessing, coverage graphs are generated from pairwise mappings using Minimap (Li, 2016) and are used to detect chimeric reads as well as reads from repetitive regions. Afterwards, the assembly graph is simplified with transitive reduction, trimming, bubble popping and a heuristic which untangles leftover junctions in the graph. As a side result, we show that the percentage of chimeric reads produced by either the Pacific Biosciences or Oxford Nanopore Technologies platforms is correlated with the read length.

de novo assembly, layout phase

nije evidentirano