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Table 3 Comparison of various features between ClinQC and QC tools

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

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

  1. aFeatures are unique in ClinQC