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AfterQC specifications

Information


Unique identifier OMICS_21400
Name AfterQC
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTQ
Biological technology Illumina, Life Technologies
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License MIT License
Computer skills Advanced
Version 0.9.6
Stability Stable
Source code URL https://codeload.github.com/OpenGene/AfterQC/tar.gz/v0.9.6
Maintained Yes

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Maintainers


  • person_outline Shifu Chen <>
  • person_outline Jia Gu <>

Publication for AfterQC

AfterQC in pipeline

2018
PMCID: 5763532
PMID: 29321003
DOI: 10.1186/s12864-017-4375-1

[…] expressed (degs) (additional file : table s4)., for mirseq the procedure was carried out differently. after automatic filtering, adapter trimming, error removing and quality control using afterqc [], good quality reads were mapped directly to mirbase (release 21) database of all mature mir sequences using novocraft’s novoalign tool. this allowed us to create raw count tables […]


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AfterQC in publications

 (2)
PMCID: 5763532
PMID: 29321003
DOI: 10.1186/s12864-017-4375-1

[…] expressed (degs) (additional file : table s4)., for mirseq the procedure was carried out differently. after automatic filtering, adapter trimming, error removing and quality control using afterqc [], good quality reads were mapped directly to mirbase (release 21) database of all mature mir sequences using novocraft’s novoalign tool. this allowed us to create raw count tables […]

PMCID: 5736589
PMID: 29259317
DOI: 10.1038/s41598-017-18072-9

[…] rna-seq data of this study has been submitted to the ncbi geo database under accession number gse106454., fastqc was used to assess the read quality. we trimmed the low quality reads by using the afterqc method. instead of using the default parameters of afterqc for trimming, we trimmed the left and right end of a read no more than 5 bp respectively to keep the number of reads and read length […]


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AfterQC institution(s)
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; HaploX BioTechnology, Shenzhen, China; University of Chinese Academy of Sciences, Beijing, China
AfterQC funding source(s)
Supported by National Science Foundation of China (No.61472411), by Technology Development and Creative Design Program of Nanshan Shenzhen (No. KC2015JSJS0028A), and by Special Funds for Future Industries of Shenzhen (No. JSGG20160229123927512).

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