What is CASPER?

CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

Merging

Main Algorithm
CASPER uses quality scores and k-mer frequency for merging.
When the difference between the quality scores of mismathcing base is significant, CASPER relies on the quality scores for correction. If not, CASPER instead examines k-mer-based contexts around the mismatch and makes a statistical decision.


Release History

version 0.8.2 (October, 2015)
  • fixs parallel processing bugs
  • needs jellyfish version 2.2.3 or higher
  • download : Source File
version 0.8.0 (March, 2014)
  • The first release of CASPER in public
  • Only targeted on amplicon sequencing
  • download : Source File

P R O G R A M

Source File v0.8.2
Binary File (for linux) v0.8.2

D A T A S E T s

Simulated Data
A4 1,000,000 reads
A5 1,000,000 reads
S4 1,000,000 reads
S5 1,000,000 reads
N4 1,000,000 reads
Real Data
C1 716,366 reads
C2 1,350,602 reads
PA 673,845 reads