From: AfterQC: automatic filtering, trimming, error removing and quality control for fastq data
 | FastQC | Trimmomatic | Cutadapt | AfterQC |
---|---|---|---|---|
Quality Control | Rich functions | Few function | Few function | Rich functions |
Auto Trimming | None | Read by read | Read by read | Global Trimming |
Cutting adapter | None | Single-end/pair-end | Single-end/pair-end | Pair-end only |
PolyX filtering | None | None | None | Supported |
Figure plotting | Static | Static | Static | Interactive |
Overlap analysis | None | Cutting adapter only | None | Supported with error correction |
Sequence error profiling | None | None | None | Supported |
Bubble detection | None | None | None | Supported |
Programming Language | Java | Java | Python | Python, C |
Speed | Fast | Fast | Fast | Fast only for single-end |