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cudamapper

The cudamapper package provides minimizer-based GPU-accelerated approximate mapping.

Library

Built as libcudamapper.[so|a]

  • Indexer module to generate an index of minimizers from a list of sequences.
  • Matcher module to find locations of matching pairs of minimizers between sequences using minimizer indices.
  • Overlapper module to generate overlaps from sequence of minimizer matches generated by matcher.

APIs documented in include folder.

Sample

sample_cudamapper - A prototypical binary highlighting the usage of libcudamapper APIs (indexer, matcher and overlapper) and techniques to tie them into an application.

Tool

cudamapper is an end-to-end command line to for sequence to sequence mapping. cudamapper outputs mappings in the PAF format and is currently optimised for all-vs-all long read (ONT, Pacific Biosciences) sequences.

To run all-vs all overlaps use the following command:

cudamapper in.fasta in.fasta

A query fasta can be mapped to a reference as follows:

cudamapper query.fasta target.fasta

To access more information about running cudamapper, run cudamapper --help.