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

Michael N. Edmonson | Zendy; Jinghui Zhang | Zendy; Chunhua Yan | Zendy; Richard P. Finney | Zendy; Daoud Meerzaman | Zendy; Kenneth H. Buetow | Zendy

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

Author(s) -

Michael N. Edmonson,

Jinghui Zhang,

Chunhua Yan,

Richard P. Finney,

Daoud Meerzaman,

Kenneth H. Buetow

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr032

Subject(s) - computer science , annotation , documentation , java , context (archaeology) , reference genome , pooling , ensembl , genome browser , genome , information retrieval , artificial intelligence , genomics , genetics , biology , programming language , gene , paleontology

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.

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