visualize and validate target mutations. Figure5 shows a demon-
stration of MutScan’s interactive mutation pileup.
MutScan is available at: https://github.com/OpenGene/
MutScan. It is written in C++ with multi-threading support. It
supports both single-end and paired-end data, and for latter one,
it will try to merge each pair with quality adjustment and error
correction.
Another tool developed by authors is FusionDirect, which can
detect gene fusions directly from raw FASTQ data. This tool also
works with FASTQ files directly and requires no alignment. It can
output fusion sites (genes and positions), along with the reads
supporting the fusions. Figure6 gives an example of the output
of FusionDirect.Fig. 5A demonstration of MutScan’s interactive HTML. The demonstrated mutation is EGFR p.T790M (hg19
chr7:55,249,071 C>T), which is an important druggable target for lung cancer. The colors of the bases
indicate the quality score (green and blue mean high quality, red means low quality). Due to page size
limitation, this figure is an incomplete screenshot. The full report can be found athttp://opengene.org/
MutScan/report.html
82 Shifu Chen et al.