new , large genomic data sets are providing more in - depth insights into the diagnosis and treatment of disease . in the past decade ,
new and innovative methods have continued to add value to the underlying data and uncover the secrets of the genome .
visual data inspection by experienced researchers is an important quality control element in the analytical process .
unfortunately , this part of the process is tedious and time consuming , and the increasing volumes of high - throughput sequencing data of various types and platforms are proving to be a major analytical challenge . here ,
we report a visualization tool that allows researchers to explore their data at a very rapid speed and significantly reduce the burden of reviewing tens and hundreds of thousands of variant calls . areas with systematic read errors can be quickly identified , and inefficient attempts to verify results in noisy regions can be avoided .
alview is a fast and portable visualization tool . the core code interfaces with heng li et al s samtools library1 for parsing bam files .
the program is written in platform - independent c. peculiarities specific to an operating system are isolated with if defined ( ifdef ) directives ; so , for instance , when microsoft visual c provides alternate support for a portable operating system interface ( posix ) standard function , a handcrafted , native interface work around is supplied . for graphical user interface ( gui ) frameworks , alview uses win32 interface for windows , the gtk2 interface for linux , and bsd unix - based systems and cocoa for apple mac os x. samtools1 is written to posix standards , but different microsoft visual compilers provide various levels of support for these unix style standards . as a result , the source code for third - party libraries that were modified for windows is provided to facilitate compiling and linking alview on windows .
the main code for alview , in the file alviewcore.cpp , is written to be portable between operating systems and emphasizes speed of execution .
the code can be compiled as a stand - alone executable and must be linked with the zlib2 and samtools1 libraries .
sequence reads are processed via custom samtools callback functions arranged in in - memory data structures and represented by an aesthetic , annotated image .
the image is then output to the screen as a native graphics object or to the disk as a standard image format file .
alview can also be compiled as a webserver daemon that uses the common gateway interface ( cgi)3 standard .
the cgi version produces interactive html output and uses dynamic html54 features , including zoom in by selection via a jquery5 library .
the cgi webserver alview version loads a list of permitted - to - access bam files from a user - maintained text file ; so custom lists of bam files of interest are easy to generate and use .
the source code is free and open to modification so that users and local system operators can implement their own security .
the alview cgi webserver version provides modifiable url access , so that , for instance , cells in a spreadsheet can link to viewable results for any sample or location .
stand - alone alview accepts parameters that specify bam file name and genomic coordinates . invoking alview in a script can create a slideshow of interesting regions .
for example , fields in a single nucleotide polymorphism ( snp ) detection output file can be used to specify a series of calls to alview to generate images for each purported polymorphism or mutation .
the burden of reviewing ten and hundreds of thousands of mutation calls can therefore be significantly reduced .
the source code is available at github.6 the readme file there points to links for selected executables and complete download packages that include the associated reference genome data .
a live webserver version of alview for examining public human cancer short - read datasets is available at https://cgwb.nci.nih.gov/cgi-bin/alview .
alview source code and executables for several operating systems are available at the national cancer institute ( nci)/national cancer informatics program s ( ncip s ) github site : https://github.com/ncip/alview .
nci retains the copyrights to  national cancer institute  and associated images , which may not be used in forked projects .
alview provides a solid substructure that allows for various types of access to short - read data across different operating systems .
figure 1 . demonstrates the various navigation and information buttons available in the web version of alview and shows how selection via mouse provides zoom in capabilities .
alview is a trim , fast , precise tool and complements existing programs such as the integrated genomics viewer ( igv),7 bamview,8 and gbrowse 2.0.9 the benefits of alview are extreme speed and a sharp focus on exploring short reads .
different implementation philosophies can influence memory usage and performance but provide useful alternative paths to solving similar problems .
igv provides much more functionality than alview by supporting many other input file types other than bam sequence read files .
igv s java implementation provides write once , run anywhere portability via implementations of the java virtual machine .
alview s implementation relies on low - level operating system and native gui toolkit api calls .
igv requires registration for download for running off of disk , whereas alview does not .
desktop igv may require internet for full , easy , simple operation , whereas alview does not require network connection ( though it may call user - invoked external webpages ) .
7 intel core i52400 cpu at 3.10 ghz and 8 gb ram , restarts of igv v2.3 took from 12 to 18 seconds .
restarts of alview took a small fraction of one second . for a small view of a genomic region ,
the java platform se binary for igv took up 292 mb , while alview took up 11 mb .
 the name alview is a contraction of the term alignment viewer . 
 alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data . 
 inputs are files of short - read sequences aligned to a reference genome in the sam / bam format and files containing reference genome data 
 . outputs are visualizations of these aligned short reads . 
 alview is written in portable c with optional graphical user interface ( gui ) code written in c , c++ , and objective - c . 
 the application can run in three different ways : as a web server , as a command line tool , or as a native , gui program . 
 alview is compatible with microsoft windows , linux , and apple os x. it is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . 
 the source code and windows / mac / linux executables are available via https://github.com/ncip/alview . 
Introduction
Features and Methods
Results