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