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)
BWA
BWA-MEM
BWA-SW
NGM
Bowtie 2

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 Length150
Read Count100000
Sequence Divergence0.0010 overall mutation rate, 0.3000 indel fraction, 1.0000 indel average length
Paired-EndYes
Insert Size100
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 150 -N 50000 --mp --ll 100 --le 50 --hi 0.000300 --hs 0.000700 --hm 1 --hM 4 --source-no-N /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.1500.300.fasta
Sampling ratio0.500
Sampling region length1500
Reference Genome File/project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
Read File(s)/project/teaser/genometeaser/tests_generated/eba4a667114e0b530a53445828381094/reads1.fastq, /project/teaser/genometeaser/tests_generated/eba4a667114e0b530a53445828381094/reads2.fastq
Gold Standard Alignment File/project/teaser/genometeaser/tests_generated/eba4a667114e0b530a53445828381094/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.