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readDepth specifications

Information


Unique identifier OMICS_00350
Name readDepth
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for readDepth

readDepth citations

 (12)
library_books

Gene based comparative analysis of tools for estimating copy number alterations using whole exome sequencing data

2017
Oncotarget
PMCID: 5432334
PMID: 28460482
DOI: 10.18632/oncotarget.15932

[…] []. additional bioinformatics tools are needed to more precisely estimate cnas from wes data., several tools have been developed for estimating somatic cnas using ngs data. for example, cnv-seq, readdepth, cnvnator, and hmmcopy use wgs data, and exomecnv, varscan2, convex, codex, conifer, and exome2cnv use wes data as inputs. control_freec, saascnv, ngcgh, and falcon use both wgs and wes [, […]

library_books

Combination inhibition of PI3K and mTORC1 yields durable remissions in orthotopic patient derived xenografts of HER2 positive breast cancer brain metastases

2016
Nat Med
PMCID: 4938731
PMID: 27270588
DOI: 10.1038/nm.4120

[…] genes in the tumors, mutation calls with less than 20 reads were excluded. r and bioconductor packages were used to prioritize and visualize the sequencing data. the segment plotting tool from the readdepth package for r was further modified to visualize cnv alterations. the sequencing data have been deposited in the national center for biotechnology information (ncbi) database of genotypes […]

library_books

Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation

2015
Sci Rep
PMCID: 4632076
PMID: 26534864
DOI: 10.1038/srep16106

[…] and details., to detect maternal cnv, chromosomes were divided into 100-kb window bins prior to obtaining the count statistics; adjacent window bins shared a 50% area of overlap. similar to various readdepth-based algorithms, the number of unique mapped reads in each window bin was counted, adjusted in terms of gc bias and mapability ratio, and then converted to a window bin z-score […]

library_books

Copy number alterations detected by whole exome and whole genome sequencing of esophageal adenocarcinoma

2015
Hum Genomics
PMCID: 4570720
PMID: 26374103
DOI: 10.1186/s40246-015-0044-0

[…] a tumor sample and its matched normal sample. these methods can be further categorized according to the study design. some commonly used ones are as follows. (a) cnvnator [], rdxplorer [], and readdepth [] detect cnas on a single tumor sample. (b) cnaseg [], segseq [], exomecnv [], hmmcopy [], and varscan2 [] identify cnas on matched tumor-normal samples. control-freec [, ] […]

library_books

Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method

2015
Sci Rep
PMCID: 4485032
PMID: 26122179
DOI: 10.1038/srep11711

[…] methods, the variability in distribution of the reads across the genome and the ability to correctly detect chromosomal aneuploidies and large cnas was compared using the bioinformatics tool readdepth. the final mps results were compared to a 180 k arraycgh profile (agilent technologies) of genomic dna of the loucy cell line which was determined prior to the experiments to serve […]

library_books

Detection of Genomic Structural Variants from Next Generation Sequencing Data

2015
Front Bioeng Biotechnol
PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] 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 (li et al., ) […]


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readDepth institution(s)
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA

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