Home - njdbickhart/RAPTR-SV GitHub Wiki

Welcome to the RAPTR-SV wiki!

#Introduction This wiki is designed to give you an introduction to RAPTR-SV by giving workflows for several common usage scenarios. It will also teach you how to install the requisite software needed for RAPTR-SV and (eventually) troubleshoot some common errors.

#General prerequisites RAPTR-SV is designed to run on Linux systems and currently requires the following programs to be installed on your path:

• Mrsfast-Ultra
• Java version 1.8

You can get more detailed information on how to install prerequisite programs and how to place them on your path within the installation page.

#Input data RAPTR-SV requires you to provide the following data in order to make SV calls:

• A reference genome fasta file indexed using MrsFast-Ultra
• One or more BAM files that were aligned with [BWA] (http://bio-bwa.sourceforge.net/)
• A list of gaps within your reference genome fasta file in BED format

Further information on input data can be found within the input data page.

#Modes RAPTR-SV currently has only two modes:

• preprocess
• cluster

Please see their respective pages for more details on usage and inputs.

#Workflows While I am not a definitive expert on analyzing sequence data, I want to provide several usage cases as examples of how to use RAPTR-SV as part of a larger analysis pipeline for detecting variants within sequence data. Below I've listed an example workflow starting from a raw fastq file to show you where RAPTR-SV will work into your analysis of sequence data. I've also included some pages describing the different output data types so that other groups can use the data generated from RAPTR-SV preprocessing in subsequent data mining programs.

An example workflow demonstrates how to use RAPTR-SV on raw sequence data.