Use IGB to

View sequence data from RNA-Seq and ChIP-seq experiments experiments

Next-generation sequencing technologies are making it much easier for individual labs to produce huge volumes of short- and long-read sequencing data. To get maximum value from these data, you often need to view the sequence reads alongside all the other known features in a genome. Using tools like BowTie and TopHat, you can align your reads onto a reference genome and then use IGB to view the alignments alongside canonical gene models provided by organizations such as The Arabidopsis Information Resource. As of IGB version 6.3., IGB can read and display short read alignments from BAM files, the binary equivalent of SAM (Sequence Alignment/Map format) files output by many alignment tools. To read more about BAM and SAM, visit the samtools Web site.

Share genomic data and annotations

It is becoming possible for many more groups to carry out genome sequencing projects. IGB makes it easy for groups to distribute and share their new genome assemblies and annotations. Using IBG's simple QuickLoad system, you can share your new genome with collaborators, keeping the data private until published, and then use the same method to share the data with the world. If you let us know about your QuickLoad site, we'll make sure that all IGB users can access it by including it in the list of default servers IGB accesses.

View data from many species and genomes

IGB can load data via the Internet using Distributed Annotation Service (DAS) ReST-style Web services, from IGB-specific QuickLoad sites, and from local files and directories. Currently, IGB accesses data provided by several sites, including our demonstration BioViz DAS and QuickLoad sites, the UCSC and Ensembl DAS sites, and others. Our BioViz data sources currently focus on supporting the Arabidopsis research community, but we plan to add support for additional genomes in the future, focusing on genomes not supported by UCSC. Data sites interested in hosting their own IGB-compatible data server sites should contact us for details.

Explore tiling array data

IGB can load data from tiling array results as genome graphs, which display probe intensity data alongside the genomic sequence. IGB supports several different tiling array data formats, including wiggle, bar, gr, sgr, and others.