NextSV is an automated pipeline for structrual variation detection from long-read sequencing. NextSV uses two aligners (Minimap2 and NGMLR) to do read mapping and uses Sniffles to do SV calling.
NanoMod is a novel computational tool for the detection of DNA modifications using Nanopore long-read sequencing data. The evaluation on simulation data with different types of modifications and on a methylation data of E. coli suggested that NanoMod achieved better performance than other existing tools in detecting modifications without training data.
PBSuite includes:
PBJelly – the genome upgrading tool.
PBHoney – the structural variation discovery tool
PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles.
PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp).