Bambino Stable

Bambino - View BAM files with this tool.

View BAM files with this tool.

Bambino is a small, simple application specially designed to offer users a graphical viewer and SNP/indel detector for next-generation sequencing files in SAM/BAM format.

The viewer post-processes unpadded BAM alignments to create a fully-padded view of the assembly, enabling complete visualization of insertions.

Bambino features :

- detects SNPs, insertions, and deletions directly from BAM files using a configurable process. This may be run from the command line (see BAM utilities documentation) or interactively from within the viewer.
- can dynamically pool data from multiple BAM files: view and analyze data from tumor/normal pairs, multiple runs, or even platforms. The variant detector takes advantage of pooling as well, producing output suitable for somatic mutation detection.
- Reconciles all indels in the dataset into a unified, padded alignment with the reference sequence, padding the reads and the reference as necessary. While the SAM/BAM specification allows for padded alignments, most BAM files contain unpadded read-mapping data. Bambino essentially converts these unpadded alignments into padded ones. This postprocessing provides a complete and unified view of the assembly, even of reads having different indel sizes at the same location. This is useful for visualizing features such as STRPs, and debugging the alignments produced by read-mapping programs.
- displays mappings of dbSNP SNP sites and reference protein sequences, using UCSC genome annotations. The database connection is configurable; it can load features from various databases and/or genome builds, and can use the UCSC public MySQL database server or a local mirror you provide.
- calculates protein coding changes caused by SNPs in NCBI RefSeqs
- can display reads against finished reference sequence (currently UCSC .2bit and .nib formats are supported), or a consensus generated from the source .bam data

Requirements:

- Java

Bambino Stable is licensed as Freeware for the Windows operating system / platform. Bambino is provided as a free download for all software users (Freeware).