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

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

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology / methods
  • Computer Graphics*
  • DNA Mutational Analysis / methods*
  • Gene Frequency
  • Genomics / methods
  • Genotype
  • Internet
  • Molecular Sequence Annotation
  • Polymorphism, Single Nucleotide
  • Sequence Alignment / methods*
  • Software*