Some paper on NGS

BamView: visualizing and interpretation of next-generation sequencing read alignments[for other viewers, see the introduction section of this paper]

Visualizing next-generation sequencing data with JBrowse

A survey of tools for variant analysis of next-generation genome sequencing data

Using GBrowse 2.0 to visualize and share next-generation sequence data

De novo assembly and genotyping of variants using colored de Bruijn graphs

GAGE: A critical evaluation of genome assemblies and assembly algorithms