Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis
Table 4
Overall evaluation and comparison of multiple aligners.
Aligners
Computational speed
Memory usage
Accuracy
Speed with single thread
Speed with multithread
Key factor impacting speed (genome size or read count)
Overall evaluation
Key factor impacting memory (Genome size or read count)
Memory usage with multithread
Sensitivity
Precision
% of multimapped
%Corrected Multi-Mapped
Bowtie1
Fast
↑
Genome size
Low
Genome size
≡
High
—
—
BWA
Fast
↑
Both
Low
Genome size
≡
BOAT
Slow
↑↑
Genome size
Low
Read count
↑↑
High
—
—
Low
GASSST
—
↑
Genome size
High★★
Genome size
≡
Low
High
—
Gnumap
Slow
↓
Genome size
High★★
Genome size
≡
GenomeMapper
Slow
≡
Genome size
Low▲
Genome size
≡
High
—
—
mrFAST
Slow
×
Genome size
High★★
Read count
×
High
—
—
mrsFAST
—
×
Genome size
Low
Read count
×
High
—
—
MAQ
—
×
Genome size
High★★
Read count
×
NovoAlign#
—
/
Read count
Low▲
Genome size
/
High
High
Low
Low
PASS
—
↑
Genome size
Low▲
Genome size
↑
High
High
Low
Low
PerM※
Fast
Genome size
Low▲
Genome size
/
Ind: low
—
Low
RazerS
Slow
×
Genome size
High★★
Read count
×
High
—
—
RMAP
—
×
Genome size
High★
Genome size
×
Mis: low
High
Low
SeqMap
—
×
Genome size
High★★★
Read count
×
High
—
—
SOAPv2
Fast
↑
Genome size
Low
Genome size
≡
High
High
Low
SHRiMAP2
Slow
↑
Genome size
High★★
Genome size
↑
High
Low
High
Segemehl
—
↑
Both
High★★★
Genome size
≡
High
—
PerM※ could adjust the threads automatically during running process. Novoalign# could support multithread only for commercial version. For computational speed, we defined the aligners which are extremely faster than others as fast, while we defined the ones which are extremely slower as slow. For memory usage, we evaluated the aligners as follow: among the s even datasets, the maximum memory usage ≤4 G, low; the maximum memory usage ≥32 G, high★★★. Low▲ represents that the maximum memory usage will have an extreme increase with H. sapiens datasets (≥4 G). ×: without multithread function. — represents medium level remark. ≡ means there is no obvious change.