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RLZAP: Relative Lempel-Ziv with Adaptive Pointers [article]

Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi and Jouni Sirén
2016 arXiv   pre-print
Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'  ...  (SPIRE 2014) then pointed out that also using relative pointers and run-length compressing them usually gives even better compression. In this paper we generalize Ferrada et al.'  ...  We then compressed the target against the reference with Ferrada et al.'s optimization of RLZ -which reflects the current state of the art, as explained in Section 1 -and with RLZAP.  ... 
arXiv:1605.04421v1 fatcat:jrbk7vqejrhh3hd7jwqyukssua

Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review

Kelvin V. Kredens, Juliano V. Martins, Osmar B. Dordal, Mauri Ferrandin, Roberto H. Herai, Edson E. Scalabrin, Bráulio C. Ávila, Rashid Mehmood
2020 PLoS ONE  
With this, it is possible to create a relative representation of positions.  ...  PPMD [99] , which is a variant of Prediction by partial matching (PPM) [100] , Range coding [101] , GZIP [102] , Log-skewed [103] , Compressed Integer Set [104] , Compressed bit vectors [105] , Lempel-Ziv-Markov  ... 
doi:10.1371/journal.pone.0232942 pmid:32453750 fatcat:mq6d6uneendw3pjdeyrplacmam