BridgeBuilder efficiently remaps BAM/SAM reads to a new reference by first building a "bridge" reference, first mapping to that bridge, and then remapping only a subset of reads to the full new reference.

The [BridgeBuilder System] 1 consists of several components, including [Baker] 2, [Binnie] 3, [Brunel] 4, & [Brindley] 5 and also relies on [samtools/htslib] 6 for SAM/BAM manipulations and is currently tested using [bwa] 7 for mapping (although it could potentially be useful for other aligners as well).

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