Skip to main content

Table 2 Benchmark comparison of long read mappers on two real data sets

From: A Long Fragment Aligner called ALFALFA

 

Illumina reads

454 reads

 

Runtime

Sensitivity

Runtime

Sensitivity

ALFALFA

5:48

99.09

0:33

99.75

BWA-MEM

5:19

99.71

1:04

99.60

BWA-SW

12:18

99.34

2:20

97.54

Bowtie 2

11:04

97.98

4:33

99.02

CUSHAW3

64:30

99.67

5:10

91.31

GEM

3:09

97.65

5:02

93.29

  1. The Illumina paired-end read data set [SRA:ERR024139] consists of 2×100 bp reads and the reads of the 454 single-end data set [SRA:SRR003161] are on average 574 bp long. Performance measures are runtime in h:mm and percentage of mapped reads (sensitivity).
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us