A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.
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Great set of tools for use with sam/bam formats. Easy to use and understand, even for the new java programmer.
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SAM tools
SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAM tools provide efficient utilities on manipulating alignments in the SAM format.
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