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).
Note: The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads 'Copyright (c) 2005, 2007- 2009, 2011-2012' should be interpreted as being identical to a statement that reads 'Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012' and a copyright statement that reads "Copyright (c) 2005-2012' should be interpreted as being identical to a statement that reads 'Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012'."