Tag: Deep-sequencing data

ReadDepth 0.9.8.4 – Detects Copy Number Aberrations in Deep Sequencing Data

ReadDepth 0.9.8.4

:: DESCRIPTION

The readDepth package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. It achieves higher accuracy than many other packages, and runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets.

::DEVELOPER

the Bioinformatics Research Laboratory at Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 ReadDepth

:: MORE INFORMATION

Citation

Miller CA, Hampton O, Coarfa C, Milosavljevic A, 2011
ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads.
PLoS ONE 6(1): e16327. doi:10.1371/journal.pone.0016327

NorahDesk 1.4 – Detecting small non-coding RNA(ncRNA) from Deep Sequencing data (RNA-seq)

NorahDesk 1.4

:: DESCRIPTION

NorahDesk is a small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data. NorahDesk utilizes the coverage-distribution of small RNA sequence data and thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes.

::DEVELOPER

NorahDesk team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Vienna RNA

:: DOWNLOAD

 NorahDesk

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep;40(16):7633-43. doi: 10.1093/nar/gks505.
Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.
Ragan C, Mowry BJ, Bauer DC.

CRISPResso v2.2.6 – Analysis of Genome Editing Outcomes from Deep Sequencing data

CRISPResso v2.2.6

:: DESCRIPTION

CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

CRISPResso

:: MORE INFORMATION

Citation

Pinello L, et al.
Analyzing CRISPR genome-editing experiments with CRISPResso.
Nat Biotechnol, 34 (7), 695-7 2016 Jul 12

Clement K, et al.
CRISPResso2 provides accurate and rapid genome editing sequence analysis.
Nat Biotechnol. 2019 Mar; 37(3):224-226. doi: 10.1038/s41587-019-0032-3. PubMed PMID: 30809026.

miRDeep2 0.1.3 / miRDeep* 3.8 – Discovering Known and Novel miRNAs from Deep Sequencing Data

miRDeep2 0.1.3 / miRDeep* 3.8

:: DESCRIPTION

miRDeep is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples. Last, a new module for preprocessing of raw Illumina sequencing data produces files for downstream analysis with the miRDeep2 or quantifier module.

miRDeep* is an integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. MiRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and SAM/BAM format.

::DEVELOPER

N. Rajewsky Lab

:: SCREENSHOTS

miRDeep

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl / java

:: DOWNLOAD

 miRDeep , miRDeep*

:: MORE INFORMATION

Citation

An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013)
miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data.
Nucleic Acids Res, 41, 727-737.

Friedländer MR., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., Rajewsky, N.
‘Discovering microRNAs from deep sequencing data using miRDeep‘,
Nature Biotechnology, 26, 407-415 (2008)

DELLY 0.8.7 – integrated Split-read and Paired-end based Structural Variant Discovery in Deep sequencing data

DELLY 0.8.7

:: DESCRIPTION

DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

::DEVELOPER

Korbel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DELLY

:: MORE INFORMATION

Citation

DELLY: structural variant discovery by integrated paired-end and split-read analysis
Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M. Stütz; Vladimir Benes; Jan O. Korbel
Bioinformatics 2012 28: i333-i339

Control-FREEC v11.6 – Control-free CNVs Detection using Deep-sequencing data

Control-FREEC v11.6

:: DESCRIPTION

Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows

:: DOWNLOAD

 Control-FREEC

:: MORE INFORMATION

Citation:

Boeva V, Popova T, Bleakley K, Chiche P, Cappo J, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Barillot E. (2012)
Control-FREEC: a tool for assessing copy number and allelic content using next generation sequencing data.
Bioinformatics. 2012 Feb 1;28(3):423-5. doi: 10.1093/bioinformatics/btr670.