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Table 6 Agreement among aligners in S2 non-trimmed data

From: How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

 

Comparison pair

Class1

Class 2

Class 3

Class 4

Randomly report one alignment per read

SOAP2 vs. Bowtie1 (2,209,957)2

95.69%

3.62%

0.69%

0.003%

SOAP2 vs.BWA (2,215,397)

95.45%

3.61%

0.69%

0.25%

Bowtie vs. BWA (2,200,129)

95.37%

3.70%

0.00%

0.25%

SOAP2 vs. Novoalign (2,436,379)

49.58%

15.40%

25.72%

9.26%

Bowtie vs. Novoalign (2,424,001)

49.81%

15.38%

25.53%

9.46%

BWA vs. Novoalign (2,428,458)

49.68%

15.44%

25.48%

9.40%

Suppress reads with multiple alignments

SOAP2 vs. Bowtie (2,085,316)

97.84%

0.00%

2.15%

0.007%

 

SOAP2 vs.BWA (2,094,218)

97.57%

0.0008%

1.99%

0.43%

 

Bowtie vs. BWA (2,052,464)

99.94%

0.00%

0.0003%

0.59%

 

SOAP2 vs. Novoalign (2,303,060)

51.37%

13.36%

25.71%

9.46%

 

Bowtie vs. Novoalign (2,283,644)

50.93%

13.35%

25.07%

10.65%

 

BWA vs. Novoalign (2,292,171)

50.86%

13.33%

25.35%

10.46%

  1. 1. Comparison pair in the format of aligner 1 vs. aligner 2.
  2. 2. Total number of reads aligned by either of these two aligners in a comparison pair.