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Protocols

SegSeq specifications

Information


Unique identifier OMICS_00352
Name SegSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained No

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Publication for SegSeq

SegSeq citations

 (19)
call_split

Comprehensive genomic analysis of Oesophageal Squamous Cell Carcinoma reveals clinical relevance

2017
Sci Rep
PMCID: 5681595
PMID: 29127303
DOI: 10.1038/s41598-017-14909-5
call_split See protocol

[…] in normal samples according to our panel of normal bams, and a threshold of greater than 1% in the Exome Aggregation Consortium (ExAC) database.Copy number alterations (CNAs) were first detected with SegSeq for 31 WGS, and GATK4 Alpha for 283 WES. GISTIC2.0 was performed to identify significantly amplified or deleted genomic regions. Hierarchical clustering was used to identify sample subtypes. St […]

library_books

Whole genome sequencing identifies a novel ALMS1 gene mutation in two Chinese siblings with Alström syndrome

2017
BMC Med Genet
PMCID: 5518093
PMID: 28724398
DOI: 10.1186/s12881-017-0418-3

[…] X-38.45 X. The mapping rate of clear data ranged from 97.03 to 97.27%, and the genome coverage ranged from 99.83% to 99.85 (Additional file : Table S5).For CNV detection, we employed a MATLAB packet, SegSeq. Only two de novo CNVs were identified in the proband. However, both CNVs were reported as polymorphisms in the Database of Genomic Variants (DGV).Single Nucleotide Variants (SNVs) were detecte […]

library_books

CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

2017
BMC Genomics
PMCID: 5371188
PMID: 28356085
DOI: 10.1186/s12864-017-3636-3

[…] 00 Genomes Project data have been shown to predict accurate copy number values due to its capability of high-resolution CNV calls []. There have been several approaches based on RD, such as MAQ [, ], SegSeq [], mrFAST [] and CNVnator []. CNVnator can overcome some disadvantages, including unique regions of the genome [, , ], poor breakpoint resolution [, , , ], and detect different sizes of CNVs, […]

call_split

Guidance to rational use of pharmaceuticals in gallbladder sarcomatoid carcinoma using patient derived cancer cells and whole exome sequencing

2016
Oncotarget
PMCID: 5354913
PMID: 28029662
DOI: 10.18632/oncotarget.14146
call_split See protocol

[…] lysis Toolkit. Point mutations were identified by MuTect, a Bayesian algorithm; short insertions and deletions determined by local assembly. To detect DNA copy-number alterations (CNAs), we performed SegSeq11 to infer somatic CNA in genomes on the basis of WES reads. Copy numbers < 1.5 were considered to indicate deletions, and those > 2.5 were considered amplifications by comparison to process ma […]

library_books

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data

2016
Int J Genomics
PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] pment of computational methods for estimating copy number alterations (CNAs). Many tools have been developed for estimating CNAs from WES data based on paired normal-tumor samples such as CNV-seq [], SegSeq [], ADTEx [], CONTRA [], EXCAVATOR [], ExomeCNV [], Control-FREEC (control-FREE Copy number caller) [], and CNVseeqer []. For example, VarScan2 [] is a computational tool that can estimate soma […]

library_books

NFIB overexpression cooperates with Rb/p53 deletion to promote small cell lung cancer

2016
Oncotarget
PMCID: 5295369
PMID: 27613844
DOI: 10.18632/oncotarget.11583

[…] sequencing across each lung tumor and liver metastasis. Matched normal tail DNA was used as a control. We were particularly interested in recurrent changes enriched in metastatic tumors. We employed Segseq [] and CNVseq [] to identify CNV changes. We did not find recurrent examples of metastasis-specific enrichment or newly acquired genetic amplifications in Mycl or deletions of Pten in the liver […]

Citations

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SegSeq institution(s)
Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA, USA; Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA; Novartis Institutes for Biomedical Research, Cambridge, MA, USA; The Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA
SegSeq funding source(s)
Supported by the US National Institutes of Health (grants 5U24CA126546 and 5U54HG003-67).

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