QC-Chain statistics

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QC-Chain specifications

Information


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

Subtool


  • Parallel-QC

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Publication for QC-Chain

QC-Chain in publications

 (9)
PMCID: 5663837
PMID: 29089539
DOI: 10.1038/s41598-017-14807-w

[…] 7 single hek293t cells, which were performed by super-seq. reads of both two data sets were used for the following analyses of circrna and snp., 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 […]

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

[…] 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 […]

PMCID: 5039670
PMID: 27677461
DOI: 10.1038/srep34420

[…] normal samples, the rna-seq data (gsm1010974) were downloaded from the reference epigenome mapping center., 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 […]

PMCID: 5025460
PMID: 27668169
DOI: 10.1016/j.atg.2016.06.001

[…] for fastq files using statistical tests (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). however, there is a vast variety of additional qc software available, such as ngs qc toolkit (), qc-chain () or chromapipe (). for specific vcf data validation and annotation, regarding variant calls, multiple realignments or genotyping, the genome analysis toolkit (gatk) represents an often […]

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

[…] 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 […]


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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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