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Bioinformatics. 2011 Mar 15;27(6):865-6. doi: 10.1093/bioinformatics/btr032. Epub 2011 Jan 28.

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.

Author information

  • 1National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. edmonson@nih.gov

Abstract

SUMMARY:

Bambino is a variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused by SNPs.

AVAILABILITY:

Bambino is written in platform-independent Java and available from https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html, along with documentation and example data. Bambino may be launched online via Java Web Start or downloaded and run locally.

PMID:
21278191
[PubMed - indexed for MEDLINE]
PMCID:
PMC3051333
Free PMC Article
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