NovelSeq statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

NovelSeq specifications


Unique identifier OMICS_02164
Name NovelSeq
Software type Package/Module, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA,FASTQ
Biological technology Illumina
Operating system Unix/Linux
Programming languages C
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.0.2
Stability No
Maintained Yes



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  • person_outline Cenk Sahinalp <>
  • person_outline Evan Eichler <>

Additional information

Publication for NovelSeq

NovelSeq in publications

PMCID: 5870608
PMID: 28881988
DOI: 10.1093/bioinformatics/btx254

[…] intensive assembly-based algorithms, only a handful of mapping and local assembly based methods for novel sequence insertion discovery are currently available. the first of such algorithms is novelseq () that we have previously developed to find insertions >200 bp using paired-end whole-genome illumina sequence data. briefly, novelseq identifies one-end anchored reads (oea), where one […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] )]. genome strip (handsaker et al., ) exploits rp, rc, sr, and population-scale patterns to detect genome structural polymorphisms., packages implementing rp and (local) as have been also reported [novelseq (hajirasouliha et al., ), hydra (quinlan et al., )] as well as tools exploiting sr and rc/rp such as svseq, mate-clever, and prism (zhang and wu, ; jiang et al., ; marschall et al., ). prism […]

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NovelSeq institution(s)
Lab for Computational Biology, Simon Fraser University, Burnaby, BC, Canada; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Cancer Agency, Genome Science Center, Vancouver, BC, Canada
NovelSeq funding source(s)
Supported by Natural Sciences and Engineering Research Council of Canada (NSERC); Bioinformatics for Combating Infectious Dieseases (BCID); Genome BC; Michael Smith Foundation for Health Research grants and US National Institutes of Health (grant U01HG005209-02).

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