Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis
Table 1
Application-specific alignment features distribution among multiple aligners.
Aligners
Operate system
Programming language
Input Format1? (Fasta and Fastq)
Output format
Multithread?
Gapped alignment?
Paired-end alignment?
Trimming alignment?
Bisulfite alignment?
Note
Bowtie
★
C++
√
SAM
√
√
√
Maximum allowed mismatches ≤3
BWA
C++
√
SAM
√
√
√
BWA-short: 200 bp; BWA-SW: 100 kbp
BOAT
C
√
*
√
√
Maximum allowed mismatches ≤3
GASSST
C++
Fasta
SAM
√
√
Merely Fasta format required for reads
Gnumap
C
√ ( prb)
SAM
√
√
√
√
Maximum read length <1000 bp
GenomeMapper
C
√
BED
√
√
Maximum read length < 2000 bp
mrFAST
★
C
√
SAM
√
√
Maximum read length <300 bp
mrsFAST
★
C
√
SAM
√
√
Maximum read length <200 bp
MAQ
C++
Fastq
map
√
Maximum read length ≤128 bp
NovoAlign
●
C++
√
SAM
√
√
√
√
√
Restrictions for academic version
PASS
C++
√ ( sff )
GFF3
√
√
√
Maximum read length <1000 bp
PerM
C++
√
SAM
√
√
√
Maximum read length ≤128 bp
RazerS
★
C++
√ ( prb)
Eland, GFF
√
√
√
Arbitrary read length
RMAP
C++
√
BED
√
√
Fixed-length reads required
SeqMap
★
C++
Fasta
Eland
√
Maximum allowed mismatches ≤5
SOAPv2
C++
√
*
√
√
√
Maximum read length <1000 bp
SHRiMAP2
Python
Fasta
SAM
√
√
√
Parallel computing supported
Segemehl
C
Fasta
*
√
√
√
√
√
Large memory usage required
SSAHA2
●
NA
√
GFF, SAM
√
For long reads mapping
We here only consider short-reads input format. Windows, Linux, or Unix operating system. ★Windows, Linux,Unix, or Mac X operating system. ●Linux,Unix, or Mac X operating system. Linux or Unix operating system.
*The short-read aligning algorithms’ own output format.
