Results Overview

Mappers were evaluated for the given test data set. The table below shows the used parameters, mapping statistics and throughput for each mapper. Detailed results for a mapper can be displayed by clicking on its name in the table or the navigation on top.

StateMapperParametersCorrectly MappedWrongly MappedNot MappedThroughput (reads/s)
Bowtie 2 (p27) -D 30 -R 20 -L 3086.922%10.957%2.121%2422
Bowtie 2 (p26) -D 30 -R 20 -L 2088.712%11.085%0.204%793
Bowtie 2 (p25) -D 30 -R 20 -L 1588.364%11.174%0.462%392
Bowtie 2 (p24) -D 30 -R 5 -L 3086.919%10.958%2.123%3223
Bowtie 2 (p23) -D 30 -R 5 -L 2088.694%11.100%0.206%1203
Bowtie 2 (p22) -D 30 -R 5 -L 1588.356%11.172%0.472%593
Bowtie 2 (p21) -D 30 -R 1 -L 3086.898%10.969%2.133%5593
Bowtie 2 (p20) -D 30 -R 1 -L 2088.589%11.160%0.252%2844
Bowtie 2 (p5) -D 5 -R 5 -L 2088.274%11.299%0.427%1420
Bowtie 2 (p4) -D 5 -R 5 -L 1585.482%11.097%3.421%758
Bowtie 2 (p7) -D 5 -R 20 -L 1585.550%11.094%3.356%466
Bowtie 2 (p6) -D 5 -R 5 -L 3086.697%11.104%2.199%3606
Bowtie 2 (p1) -D 5 -R 1 -L 1585.140%10.964%3.896%2219
Bowtie 2 (p3) -D 5 -R 1 -L 3086.678%11.102%2.220%6718
Bowtie 2 (p2) -D 5 -R 1 -L 2088.166%11.299%0.536%3719
NGM88.453%11.004%0.543%4292
Bowtie 2 (p9) -D 5 -R 20 -L 3086.696%11.106%2.198%2599
Bowtie 2 (p8) -D 5 -R 20 -L 2088.294%11.287%0.419%887
BWA-MEM88.948%11.030%0.022%3020
BWA-SW85.064%11.202%3.734%2475
BWA88.047%10.956%0.997%3843
Bowtie 2 (def)88.412%11.200%0.388%2722
Bowtie 2 (p16) -D 15 -R 20 -L 1587.672%11.248%1.080%424
Bowtie 2 (p17) -D 15 -R 20 -L 2088.582%11.164%0.254%833
Bowtie 2 (p14) -D 15 -R 5 -L 2088.563%11.178%0.259%1324
Bowtie 2 (p15) -D 15 -R 5 -L 3086.849%11.012%2.139%3386
Bowtie 2 (p12) -D 15 -R 1 -L 3086.826%11.023%2.151%6045
Bowtie 2 (p13) -D 15 -R 5 -L 1587.628%11.265%1.107%678
Bowtie 2 (p10) -D 15 -R 1 -L 1587.333%11.294%1.373%1754
Bowtie 2 (p11) -D 15 -R 1 -L 2088.455%11.226%0.318%3236
Bowtie 2 (p18) -D 15 -R 20 -L 3086.847%11.017%2.136%2483
Bowtie 2 (p19) -D 30 -R 1 -L 1588.112%11.242%0.646%1385

The figure below visualizes above results by directly comparing accuracy and throughput. The optimal mapper showing both highest accuracy and throughput, if any, will be located in the top right corner.

Data Set

This section contains information on the benchmark data set.

Simulation Overview

Input Data SourceSimulated data set (created using Teaser)
Sequencing Platformillumina
Read Length60
Read Count250000
Sequence Divergence0.0010 overall mutation rate, 0.3000 indel fraction, 1.0000 indel average length
Paired-EndNo
Insert SizeNone
Reads by Edit DistanceThe edit distance of a read is calculated as the total number of bases that are different to the reference. This includes mutations and sequencing errors.

Simulation Details

Subsampling enabledYes
Simulator/project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 250000 --ll 500 --le 50 --hi 0.000300 --hs 0.000700 --hm 1 --hM 4 --source-no-N /project/teaser/genometeaser/references/Danio_rerio.fa.sampled.100.600.120.fasta
Sampling ratio0.010
Sampling region length600
Reference Genome File/project/teaser/genometeaser/references/Danio_rerio.fa
Read File(s)/project/teaser/genometeaser/tests_generated/2f0c57c71491a10902c3dff32a47df66/reads.fastq
Gold Standard Alignment File/project/teaser/genometeaser/tests_generated/2f0c57c71491a10902c3dff32a47df66/mapping_comparison.sam
Mapping Statistics

This plot shows the fractions of correctly, wrongly and not mapped reads for each mapper and the selected mapping quality cutoff. Reads that have been filtered using the mapping quality cutoff are shown as unmapped. The interactive legend can be used to, for example, display only the number of wrongly and not mapped reads.

Edit Distance

This plot shows the effect of the number of mismatches introduced in reads on mapping rates.

Mapping Quality

This section represents an overview of the distribution of mapping quality values for all mappers. A detailed evaluation of mapping qualities for specific mappers can be found on the respective mapper results page (accessible using the navigation on top). The first plot rates each mapping quality threshold (0-255) by comparing the numbers of wrongly and correctly mapped reads that would be removed due to falling under the threshold. The second plot shows the total number of mapped reads for each mapping quality threshold (all reads with a mapping quality value smaller or equal to the threshold).

 

MAPQ ROC

Precision and Recall
Correctly Mapped/s
Memory Usage