CR-index

Compressed read index - bioinf data structure for fast querying substring in reads.

Installation

Dependencies

• SGA
• SDSL
• Boost (widely available as system package)
• PStreams (widely available as system package)
• libboost - "libboost-filesystem" and "libboost-system" libs

Installation

make examples compiles examples and all dependencies

TODO

• test e-coli bacteria
• implement bloom filter?
  • https://github.com/mavam/libbf
  • https://code.google.com/p/bloom/

Benchmark

• 6M reads (generated from yarrowia.fasta), read length 100, 1% of errors
  • 352K critical reads
  • superstring compress ratio 2.59
  • superstring size 231M (1.85M reads were missing)
  • RSS ~ 300MB