Super deduper, fast PCR duplicate detection in fastq files. - Kristen R. Petersen; David A. Streett; Alida T. Gerritsen; Samuel S. Hunter; Matthew L. Settles (BCB, 2015)

expHTS: analysis of high throughput sequence data in an experimental framework. - David A. Streett; Kristen R. Petersen; Alida T. Gerritsen; Samuel S. Hunter; Matthew L. Settles (BCB, 2015)

SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing. - Ilya Y. Zhbannikov; Samuel S. Hunter; James A. Foster; Matthew L. Settles (BCB, 2017)