A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-10-10, 14:56
based on data in:
/home/shared/16TB_HDD_01/graceac9/project-pycno-multispecies-2023/output/26-hisat2-pycno-d6-d12
General Statistics
Showing 24/24 rows.| Sample Name | % Aligned |
|---|---|
| PSC-0519-hisat | 79.2% |
| PSC-0525-hisat | 79.4% |
| PSC-0531-hisat | 78.5% |
| PSC-0537-hisat | 77.7% |
| PSC-0549-hisat | 80.9% |
| PSC-0561-hisat | 81.7% |
| PSC-423-hisat | 82.0% |
| PSC-426-hisat | 80.8% |
| PSC-429-hisat | 81.3% |
| PSC-432-hisat | 83.0% |
| PSC-435-hisat | 82.3% |
| PSC-438-hisat | 82.4% |
| PSC-441-hisat | 82.3% |
| PSC-444-hisat | 82.2% |
| PSC-453-hisat | 83.6% |
| PSC-456-hisat | 81.8% |
| PSC-465-hisat | 82.7% |
| PSC-468-hisat | 81.8% |
| PSC-522-hisat | 80.7% |
| PSC-528-hisat | 81.7% |
| PSC-534-hisat | 81.9% |
| PSC-540-hisat | 82.8% |
| PSC-552-hisat | 83.5% |
| PSC-564-hisat | 81.8% |
Bowtie 2 / HiSAT2
Bowtie 2 and HISAT2 are fast and memory-efficient tools for aligning sequencing reads against a reference genome. Unfortunately both tools have identical log output by default, so it is impossible to distiguish which tool was used. .DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4.
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
