Skip to main content

Table 4 Comparison of meta-methods

From: MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

 (a) Percent of one million 251 bp reads mapped correctly to theE.coli genome. Shown in parenthesis are incorrectly mapped
reads and remaining are rejected  
Div NextGenMap+ NextGenMap+ NextGenMap+ NextGenMap+
  MaxSSmap_fast MaxSSmap CUDASW++ SSW
    Reads without gaps  
.1 96 (1.3) 97 (1.4) 97 (1) 97 (2.8)
.2 95 (1.5) 96.7 (1.5) 96 (1) NA
.3 91 (1.4) 94.8 (1.3) 93 (1.5) NA
    Reads with gaps  
.1 92 (1.5) 95.7 (1.4) 97 (1) 97.2 (2.8)
.2 92 (2.1) 94 (2.5) 95 (2) NA
.3 82 (2.9) 90.5 (3.5) 92.5 (1.6) NA
(b) Time in minutes to map one million 251 bp reads to the E.coli genome
Div NextGenMap+ NextGenMap+ NextGenMap+ NextGenMap+
  MaxSSmap_fast MaxSSmap CUDASW++ SSW
    Reads without gaps  
.1 25 34 197 1397
.2 57 77 537 NA
.3 148 204 1343 NA
    Reads with gaps  
.1 38 60 413 2601
.2 68 109 756 NA
.3 162 222 1528 NA
  1. See Table 3 caption for details about reads. NA denotes time greater than 48 hours which is our cutoff time on this data.