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.
Link to Github: https://github.com/k-medai/CASPER

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 0.8.3 (February, 2024)
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 v0.8.3
Binary File (for linux) v0.8.3

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