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.
| State | Mapper | Parameters | Correctly Mapped | Wrongly Mapped | Not Mapped | Throughput (reads/s) |
|---|---|---|---|---|---|---|
| NextGenMap 0.5.3 (revcomp) | 91.633% | 8.361% | 0.006% | 22709 | ||
| NextGenMap 0.5.2 (current) | 91.633% | 8.361% | 0.006% | 24693 | ||
| NextGenMap 0.4.13 | 91.675% | 8.324% | 0.002% | 23472 | ||
| BWA | 15.717% | 1.449% | 82.834% | 18887 | ||
| BWA-MEM | 91.556% | 8.367% | 0.078% | 8637 | ||
| BWA-SW | 87.182% | 8.751% | 4.067% | 6729 | ||
| Bowtie 2 | 84.730% | 8.029% | 7.242% | 17633 |
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.
Simulation Overview
| Input Data Source | Simulated data set (created using Teaser) |
|---|---|
| Sequencing Platform | illumina |
| Read Length | 150 |
| Read Count | 239543 |
| Sequence Divergence | 0.0500 overall mutation rate, 0.3000 indel fraction, 1.0000 indel average length |
| Paired-End | No |
| Insert Size | None |
| Reads by Edit Distance | The 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 enabled | Yes |
|---|---|
| Simulator | /project2/NextGenMapTest/Teaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 239543 --ll 500 --le 50 --hi 0.015000 --hs 0.035000 --hm 1 --hM 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta.sampled.4.1500.300.fasta |
| Sampling ratio | 0.250 |
| Sampling region length | 1500 |
| Reference Genome File | /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta |
| Read File(s) | /project2/NextGenMapTest/Teaser/tests_generated/D2_n/reads.fastq |
| Gold Standard Alignment File | /project2/NextGenMapTest/Teaser/tests_generated/D2_n/mapping_comparison.sam |
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.
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).