See for the new 1.x releases of SAMtools, BCFtools, and HTSlib. This website contains information pertaining to the old 0.1.19 samtools release, and so is useful but somewhat out of date. As time permits, this information will be updated for the new samtools/bcftools versions and moved to the new website.

Text Alignment Viewer

Although from pileup output we can get a rough idea about how well reads are aligned, closer investigation requires a descent alignment viewer. SAMTools implements a very simple text alignment viewer based on the GNU ncurses library.

This alignment viewer works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice. SAMTools viewer is known to work with an 130GB alignment swiftly. Due to its text interface, displaying alignments over network is also very fast. Here are two screenshots of two pieces of alignments: