From: ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research
Features | ClinQC v1.0 | CANGS v1.1 | TagCleaner v0.16 | SolexaQA v3.1.3 | FASTX-Toolkit v0.0.13 | TagDust | PRINSEQ v0.20.4 | FastQC v0.11.3 | NGSQCTookit v2.3.3 | QC-Chain v1.0 |
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Analysis of several datasets in a single run | yes | no | no | no | no | no | no | no | no | yes |
Analysis of all platforms in single runa | yes | no | no | no | no | no | no | no | no | no |
Virtual Machinea | yes | no | no | no | no | no | no | no | no | no |
Sanger format conversiona | yes | no | no | no | no | no | no | no | no | no |
Sanger base callinga | yes | no | no | no | no | no | no | no | no | no |
Sanger QCa | yes | no | no | no | no | no | no | no | no | no |
Sanger primer trimminga | yes | no | no | no | no | no | no | no | no | no |
Installation required | no | yes | yes | yes | yes | yes | yes | no | no | yes |
Supported sequencing platforms | Sanger, Illumina, 454, Ion torrent | 454 | Illumina, 454 | Illumina | Illumina | Illumina, 454 | Illumina, 454 | any in FASTQ format | Illumina, 454 | NGS |
Parallel processing | yes | no | no | no | no | yes | no | yes | yes | yes |
Format conversion | yes | no | no | no | yes | no | no | no | yes | yes |
Primer/Adapter trimming | yes | yes | yes | no | yes | yes | no | no | yes | yes |
Ns trimming | yes | yes | yes | no | no | yes | yes | no | yes | yes |
Demultiplexing | yes | yes | yes | yes | yes | yes | no | no | no | yes |
Detection of file format | yes | no | no | yes | no | no | yes | no | yes | yes |
Dependencies | yes | yes | no | yes | yes | no | yes | no | yes | no |
Graphical QC report | yes | no | no | yes | yes | no | yes | yes | yes | yes |
Duplicate removal | yes | no | yes | no | yes | no | yes | no | no | yes |
Contamination filtering | yes | no | yes | no | no | yes | yes | no | no | yes |
GC content assessment | yes | no | yes | no | yes | no | yes | yes | yes | yes |