NCLscan statistics

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Citations per year

Number of citations per year for the bioinformatics software tool NCLscan

Tool usage distribution map

This map represents all the scientific publications referring to NCLscan per scientific context
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Associated diseases


Popular tool citations

chevron_left Circular RNA detection Gene fusion detection chevron_right
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NCLscan specifications


Unique identifier OMICS_10194
Name NCLscan
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.3
Stability Stable
Bedtools, Samtools, BLAT, BWA, Novoalign, novoindex
Maintained Yes


No version available



  • person_outline Trees-Juen Chuang

Publication for NCLscan

NCLscan citations


Current Research on Non Coding Ribonucleic Acid (RNA)

PMCID: 5748684
PMID: 29206165
DOI: 10.3390/genes8120366

[…] dentification of the new circRNAs from RNA-seq data. Notable circRNA identification tools are find_circ [], MapSplice2 [], Segemehl [], circExplorer [], circRNA_finder [], CIRI [], ACFS [], KNIFE [], NCLscan [], DCC [] and UROBORUS []. Information regarding these tools is listed in . In addition, CircView, a platform visualization tool, is specifically developed to visualize circRNAs detected from […]


Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers

Int J Genomics
PMCID: 5733622
PMID: 29349062
DOI: 10.1155/2017/6218353

[…] when segmented reads are mapped in a noncolinear manner [, ]. As described by Zeng et al. [], the tools that use the pseudo-reference-based approach to detect circRNAs include PTESFinder, KNIFE, and NCLscan, whereas circRNA_finder, CIRCexplorer, DCC, find_circ, UROBORUS, CIRI, MapSplice, and segemehl utilize the fragmented-based approach. In addition, several integrated tools aimed to identify ci […]


Circular RNAs (circRNAs) in Health and Disease

PMCID: 5748671
PMID: 29182528
DOI: 10.3390/genes8120353

[…] hese tools can recognize circRNA sequences from RNA-Seq data based on two different strategies. One approach is the candidate-based approach, also known as the pseudo-reference based approach. KNIFE, NCLScan, and PTESFinder all abide by this approach where putative circRNA sequences need to be provided with information for gene annotation. Although KNIFE can directly retrieve back-spliced junction […]


A comprehensive overview and evaluation of circular RNA detection tools

PLoS Comput Biol
PMCID: 5466358
PMID: 28594838
DOI: 10.1371/journal.pcbi.1005420
call_split See protocol

[…] increased with thresholds for read counts, but some highly expressed false positives were also reported by several tools, leading to a fluctuation of precision at the end. Also, we could observe that NCLScan consistently dominated other tools regarding the precision measure. Meanwhile, KNIFE, Segemehl, CIRI, PTESFinder and CIRCexplorer achieved the best sensitivity. Consistent with the F1 measure, […]

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NCLscan institution(s)
Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei, Taiwan
NCLscan funding source(s)
Genomics Research Center, Academia Sinica, Taiwan (internal funding); Ministry of Science and Technology (MOST), Taiwan [MOST 103-2628-B-001-001-MY4, MOST 103-2911-I-001-507]

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