PT - JOURNAL ARTICLE AU - David E. Hufnagel AU - Matthew B. Hufford AU - Arun S. Seetharam TI - SequelTools: A Suite of Tools for Working with PacBio Sequel Raw Sequence Data AID - 10.1101/611814 DP - 2019 Jan 01 TA - bioRxiv PG - 611814 4099 - http://biorxiv.org/content/early/2019/12/19/611814.short 4100 - http://biorxiv.org/content/early/2019/12/19/611814.full AB - Background PacBio sequencing is an incredibly valuable third-generation DNA sequencing method due to very long read lengths, ability to detect methylated bases, and its real-time sequencing methodology. Yet, hitherto no tool was available for analyzing the quality of, subsampling, and filtering PacBio data.Results Here we present SequelTools, a command-line program containing three tools: Quality Control, Read Subsampling, and Read Filtering. The Quality Control tool quickly processes PacBio Sequel raw sequence data from multiple SMRTcells producing multiple statistics and publication-quality plots describing the quality of the data including N50, read length and count statistics, PSR, and ZOR. The Read Subsampling tool allows the user to subsample reads by one or more of the following criteria: longest subreads per CLR or random CLR selection. The Read Filtering tool provides options for normalizing data by filtering out certain low-quality scraps reads and/or by minimum CLR length. SequelTools is implemented in bash, R, and Python using only standard libraries and packages and is platform independent.Conclusions SequelTools is a program that provides the only free, fast, and easy-to-use quality control tool, and the only program providing this kind of read sumbsampling and read filtering for PacBio Sequel raw sequence data, and is available at https://github.com/ISUgenomics/SequelToolsBAMbinary alignment/map formatCLRcontinuous long readCPUCentral Processing UnitPDFportable document formatPSRpolymerase-to-subread ratioQCQuality ControlRAMRandom-access memorySAMsequence alignment/map formatSMRTSingle Molecule Real Time sequencing technologZMWzero-mode waveguideZORzero-mode waveguide occupancy ratio