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rSW-seq specifications


Unique identifier OMICS_00351
Name rSW-seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Peter J. Park

Publication for rSW-seq

rSW-seq citations


Detection of Genomic Structural Variants from Next Generation Sequencing Data

Front Bioeng Biotechnol
PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] e regions of the same length.A considerable number of methods for the detection of CNV in whole-genome sequencing (WGS) data have been reported in the literature, including CNVnator, CNAnorm, CNAseg, rSW-seq, cn.MOPS, JointSLM, ReadDepth, and BIC-seq (Ivakhno et al., ; Kim et al., ; Abyzov et al., ; Magi et al., ; Miller et al., ; Xi et al., ; Gusnanto et al., ; Klambauer et al., ). Recently, PSCC […]


PSCC: Sensitive and Reliable Population Scale Copy Number Variation Detection Method Based on Low Coverage Sequencing

PLoS One
PMCID: 3897425
PMID: 24465483
DOI: 10.1371/journal.pone.0085096

[…] he read counts method can achieve a high resolution in a relatively low coverage sequencing, and some recently popular algorithms are based on it, including SegSeq , CNV-seq , CNAseg , ReadDepth and rSW-seq . However, most of these algorithms need one real or theoretical comparative genome, which induce an additional cost or unexpected fluctuations that prevent further large-scale association res […]


Computational tools for copy number variation (CNV) detection using next generation sequencing data: features and perspectives

BMC Bioinformatics
PMCID: 3846878
PMID: 24564169
DOI: 10.1186/1471-2105-14-S11-S1

[…] vals with deletion and insertion events using corrected Z-scores. The tool SegSeq requires a predefined amount of reads mapped in a genomic window []. Similar to SegSeq, recursive Smith-Waterman-seq (rSW-seq) was developed for CNV detection in matched tumor-control samples []. Different from SegSeq, rSW-seq does not rely on predefined genomic windows. It first sorts reads according their genomics […]


Mediation of Drosophila autosomal dosage effects and compensation by network interactions

Genome Biol
PMCID: 3446302
PMID: 22531030
DOI: 10.1186/gb-2012-13-4-r28

[…] sing HTSeq union mode [], and used the unique mapping reads to calculate reads per kb per million mapped (RPKM) as the normalized metric of gene expression. We identified the novel Df breakpoint with rSW-Seq [] and determined fold-difference for aneuploid segments with samtools [], which we expressed as reads per million (RPM). All but the smallest 5 kb deletion was detected using this method. We […]


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rSW-seq institution(s)
Center for Biomedical Informatics, Harvard Medical School, MA, USA

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