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"SAM\n\nA SAM file (.sam) is a tab-delimited text file that contains sequence alignment data. A BAM file (.bam) is the binary version of a SAM file. These formats are described on the SAM Tools web site: http://samtools.sourceforge.net.\n\nIndexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention. Specifically, a BAM index file should be named by appending ".bai" to the bam file name. A SAM index filename is created by appending ".sai". In both cases the index files must reside in the same directory as the BAM or SAM file. \n\nTools for sorting and indexing BAM files are available at the SAM Tools website referenced above. SAM files can be sorted and indexed using the igvtools package. \n\nChromosome names: Chromosome names must be consistent across all annotation and data files. For convenience, IGV equates chromosome numbers and names of the form chr# (e.g. 1 and chr1 are equivalent).\n\nOne-based index: Start and end positions are identified using a one-based index. The end position is included. For example, setting start-end to 1-2 describes two bases, the first and second in the sequence."

Dominating the Next Generation Sequencing data analysis challenge\n\nWe have overcome the challenge to analyze Next Generation Sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user-interface.\nCLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.