bambam

We have hosted the application bambam in order to run this application in our online workstations with Wine or directly.

Quick description about bambam:

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: