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Table 3 Performances of algorithms in mapping FASTQ files of different size with large reference libraries.

From: NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective

Library Algorithm FASTQ Time Performances   Mapping parameters  
acronym sequences   strain reads Mapping time (sec) CPU-time (sec) used reads unused reads Matches min pairwise identities max pairwise ideniies
  15,565 BTL A 21,238 63 33,34 18,274 2,964 684 74,00% 100%
CBS    B 58,263 99 123 54,822 3,441 661 91,00% 100%
ITS   BBm A 21,238 80 39,82 18,323 2,915 626 68,20% 100%
    B 58,263 114 49,57 55,675 2,588 708 62,30% 100%
  34,683 BTL A 21,238 186 104 19,163 2,075 2,051 73,40% 100%
CBS    B 58,263 273 393 57,140 1,123 2,457 79,50% 100%
ITS-LSU   BBm A 21,238 204 109 19,000 2,238 1,939 58,80% 100%
    B 58,263 311 161 56,930 1,333 2,445 63,60% 100%
  2,727 BTL A 21,238 16,7 13,59 13,904 7,334 319 74,10% 100%
ISHAM    B 58,263 30,3 33,5 36,416 21,847 297 82,00% 100%
ITS   BBm A 21,238 37,7 16,13 13,665 7,573 280 74,50% 100%
    B 58,263 45,2 26,03 35,653 22,610 305 85,70% 100%
  1. Strain A: CMC 1793; strain B: CMC 1818.