NCLscan statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

Associated diseases

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


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  • person_outline Trees-Juen Chuang <>

Publication for NCLscan

NCLscan in publications

PMCID: 5748684
PMID: 29206165
DOI: 10.3390/genes8120366

[…] 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 […]

PMCID: 5748671
PMID: 29182528
DOI: 10.3390/genes8120353

[…] 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 […]

PMCID: 5466358
PMID: 28594838
DOI: 10.1371/journal.pcbi.1005420

[…] 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 […]

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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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