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

@article{Edmonson2011BambinoAV,
  title={Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format},
  author={Michael N. Edmonson and Jinghui Zhang and Chunhua Yan and Richard P. Finney and Daoud M. Meerzaman and Kenneth H. Buetow},
  journal={Bioinformatics},
  year={2011},
  volume={27 6},
  pages={
          865-6
        }
}
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… 

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References

SHOWING 1-10 OF 11 REFERENCES

The Sequence Alignment/Map format and SAMtools

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by

The UCSC Genome Browser database: update 2011

New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track.

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

MagicViewer is a sophisticated assembly visualization and genetic variation annotation tool for next-generation sequencing data, which can be widely used in a variety of sequencing-based researches, including genome re-sequencing and transcriptome studies.

The UCSC Genome Browser database: update 2010

The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated

Consed: a graphical tool for sequence finishing.

A finishing tool, consed, which attempts to implement principles of shotgun sequencing by using error probabilities from phred and phrap as an objective criterion to guide the entire finishing process.

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

VarScan is presented, an open source tool for variant detection that is compatible with several short read aligners that demonstrates its ability to detect SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples.

Reliable identification of large numbers of candidate SNPs from public EST data

The SNPpipeline, a polymorphism detection system that uses public-domain sequence data, has identified more than 3,000 candidate single-nucleotide polymorphisms (SNPs) and suggests that existing sequence resources may serve as a valuable source for identifying genetic variation.

Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not

The UCSC Genome Browser Database: update 2006

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data.

Fast and accurate short read alignment with Burrows–Wheeler transform

Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.