Bioinformatics Toolbox provides algorithms and visualization techniques for Next Generation Sequencing analysis. The toolbox enables you to analyze whole genomes while performing calculations at a base pair level of resolution. You can use the NGS browser to visualize and investigate short-read alignments using either single-end or paired-end short reads. You can also build custom analysis routines, as shown in the following examples.
Using the NGS browser, you can verify and investigate the alignment of short-read sequences in support of analyses that measure genetic variation and gene expression. The NGS browser lets you:
The data sets used in Next Generation Sequencing analysis are often too large to fit into physical memory. Bioinformatics Toolbox provides specialized data containers that enable you to analyze entire genomes.
BioIndexedFile object lets you access the contents of text files containing nonuniform-sized entries such as sequences, annotations, and cross references to the data set. You can generate these objects from tables, flat files, or application-specific formats such as SAM, FASTA, and FASTQ.
BioMap class stores information from short-read sequences, including sequence headers, read sequences, quality scores, and data about alignment and mapping to a single reference sequence. You can use object properties and methods to explore, access, filter, and manipulate the data contained in a