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QC-Chain specifications


Unique identifier OMICS_01070
Name QC-Chain
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output data FASTQ
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.0
Stability No
Maintained No


  • Parallel-QC


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Publication for QC-Chain

QC-Chain citations


Heterogeneous circRNA expression profiles and regulatory functions among HEK293T single cells

Sci Rep
PMCID: 5663837
PMID: 29089539
DOI: 10.1038/s41598-017-14807-w

[…] Quality filtering on these reads was performed using Parallel-QC and sequences which did not fulfill the following criteria were discarded: reads with quality score ≥ 20, the GC proportion ranged from 0.4 to 0.6. All the downstream analyses were based o […]


Feed additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken

PMCID: 5541433
PMID: 28768551
DOI: 10.1186/s40168-017-0315-1
call_split See protocol

[…] n 400 bp or longer than 800 bp, as well as sequences containing fewer than two primer mismatches, uncorrectable barcodes, ambiguous bases, or homopolymer runs in excess of 8 bases, were removed using Parallel-QC [] and QIIME []. Then the sequences were checked for chimeras using UCHIME [] and assigned to operational taxonomic units (OTUs) using Parallel-META [, ] with a 97% threshold of pairwise i […]


Single cell SNP analyses and interpretations based on RNA Seq data for colon cancer research

Sci Rep
PMCID: 5039670
PMID: 27677461
DOI: 10.1038/srep34420

[…] The single-cell RNA-Seq raw data were processed through stringent quality control using Parallel-QC, a parallel quality control computational engine for NGS data. In this quality process, we only considered uniquely mappable reads with a trim quality value of no less than 20 and a thresh […]


The influence of trematode parasite burden on gene expression in a mammalian host

BMC Genomics
PMCID: 4982272
PMID: 27514777
DOI: 10.1186/s12864-016-2950-5

[…] quences may negatively influence downstream analyses and lead to erroneous inferences []. We suggest filtering out such sequences using metagenomics databases, contaminant removal software (DeconSeq, QC-chain, [, ]), and genomic features such as GC content and codon usage bias to identify potential non-target sequences. […]


Large scale contamination of microbial isolate genomes by Illumina PhiX control

Stand Genomic Sci
PMCID: 4511556
PMID: 26203331
DOI: 10.1186/1944-3277-10-18

[…] ams have been designed for analyzing NGS data such as TileQC [], FastQC [], PRINSEQ [], NGS-QC [], programs to detect contamination such as DeconSeq [], as well as multi genome alignment (MGA) [] and QC-Chain [] which can provide both rapid QC and contamination filtering of NGS data. Such programs are meant to prevent release of contaminated sequences. However, our results from scanning publicly a […]


Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis

Genome Biol
PMCID: 4378019
PMID: 25853185
DOI: 10.1186/s13059-015-0597-1

[…] pping, normalization, peak-calling, assessment of reproducibility among biological replicates, and post-processing of peaks []. Low-quality reads in the raw data (FASTQ files) were filtered out using Parallel-QC 1.0 []. Reads kept were then mapped to the A. thaliana genome (TAIR10) using Bowtie [] version 2.0.2 under default parameters. Technical replicates showed very high similarity and were com […]

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QC-Chain institution(s)
CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China; College of Computer and Information Technology, China Three Gorges University, Yichang, Hubei, China

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