SegSeq protocols

SegSeq specifications


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


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Publication for SegSeq

SegSeq IN pipelines

PMCID: 5518093
PMID: 28724398
DOI: 10.1186/s12881-017-0418-3

[…] 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 1: 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) […]

PMCID: 4716855
PMID: 26819646
DOI: 10.7150/jca.13150

[…] including insertions, deletions, inversions and translocations of chromosome bands or arms). copy number variations (cnvs) were detected by an in-house program with an algorithm similar to software segseq 32 of broad institute. ebv integrations were also detected by an in-house program. after the variations were detected, annovar 33 was used to do annotation and classification., first, […]

PMCID: 4352754
PMID: 25425480
DOI: 10.1038/ncomms6507

[…] from gatk and further filtered on exon targets and individual sample genotypes were filtered on a genotype quality score of 50. copy-number alterations were detected based on sequence-read depths by segseq29; chromosomal rearrangements were detected from clusters of discordantly mapped reads with inferred insert size longer than 1 kb or mapped to different chromosomes. the observation […]

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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