nvBWT

nvBWT is an application built on top of NVBIO to perform BWT-based reference indexing for nvBowtie and potentially other FM-index based applications.

Given one or multiple fasta files, it will create both the forward and reverse BWT as well as 2-bit packed representation of the files and a few other auxiliary indices:

*  ./nvBWT my-reference.fasta my-index
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will generate the following files:

*  my-index.pac
*  my-index.rpac
*  my-index.bwt
*  my-index.rbwt
*  my-index.sa
*  my-index.rsa
*  my-index.ann
*  my-index.amb
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Performance

nvBWT runs the BWT construction on the GPU, using newly developed parallel algorithms. Here's a graph showing its superior performance compared to two other popular CPU based BWT builders:

Options

nvBWT supports the following command options:

*    nvBWT [options] input_file output-prefix
*    options:
*     -v       | --verbosity     int (0-6) [5]          // select the verbosity level
*     -m       | --max-length    int       [inf]   // clamp input length
*     -b       | --byte-packing                    // output a byte-encoded .pac file
*     -w       | --word-packing                    // output a word-encoded .wpac file (more efficient)
*     -c       | --crc                             // compute CRCs
*     -d                | --device                                                      // select a cuda device
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