This is the Linux app named BamBam whose latest release can be downloaded as bambam-1.4.tgz. It can be run online in the free hosting provider OnWorks for workstations.
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BamBam
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DESCRIPTION
BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more.
Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball.
Features
- call SNPs and indels
- impute genotypes
- build consensus sequences
- tabulate counts of mapped reads (RNA-seq)
- infer haplotype phasing with K-means clustering
- analyze DNA methylation (bisulfite-sequencing)
Audience
Science/Research
Programming Language
Perl, C++
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/bambam/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
