LargeDEL 0.1 – A large Deletion Finder tool

LargeDEL 0.1

:: DESCRIPTION

LargeDEL is a software to find large deletions on the aligned whole genome sequence data. It is also capable of extracting the candidate deletions according to desired criteria.

::DEVELOPER

Advanced Genomics and Bioinformatic Research Group, İGBAM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

LargeDEL

:: MORE INFORMATION

SVseq 2.2 – Detecting exact Breakpoints of Deletions with Low-coverage Sequence data

SVseq 2.2

:: DESCRIPTION

SVseq2 is an improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SVseq2

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S6. doi: 10.1186/1471-2105-13-S6-S6.
An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.
Zhang J1, Wang J, Wu Y.

LINDEL – Integrated Design system for LincRNA deletion

LINDEL

:: DESCRIPTION

LINDEL is the Integrated Design system for LincRNA deletion (LINDEL) , which was implemented on an interactive web genome-browser. LINDEL system makes possible the design of sgRNAs that i) are based on improved annotations of human and mouse lincRNA genes, ii) function as pairs for the deletion of both whole and segmental regions of these genes, again based on comprehensive functional annotations, and iii) efficiently generate mutations because of both sequence- and secondary structure-based features.

:: DEVELOPER

BIG Lab. (BIOINFORMATICS & GENOMICS)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Lee HJ, Gopalappa R, Sunwoo H, Choi SW, Ramakrishna S, Lee JT, Kim HH, Nam JW.
En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements.
Nucleic Acids Res. 2019 May 7;47(8):3875-3887. doi: 10.1093/nar/gkz109. PMID: 30783652; PMCID: PMC6486550.

ExonDel 1.07 – Detection of Internal Exon Deletion with Exon Del

ExonDel 1.07

:: DESCRIPTION

ExonDel is a tool designed specially to efficiently detect exon deletions.

::DEVELOPER

ExonDel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • R
  • Perl

:: DOWNLOAD

 ExonDel

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Oct 16;15:332. doi: 10.1186/1471-2105-15-332.
Detection of internal exon deletion with exon Del.
Guo Y1, Zhao S, Lehmann BD, Sheng Q, Shaver TM, Stricker TP, Pietenpol JA, Shyr Y.

Clippers 0.0.9 – Deletion Identification Program using Periodic Spaced Seed

Clippers 0.0.9

:: DESCRIPTION

Clippers is a program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads. Currently, Clippers is implemented for long reads Illumina, ex: 75bp or 100bp, allowing mismatches and a single deletion/splicing.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

  Clippers

:: MORE INFORMATION

Citation:

Yangho Chen, Tade Souaiaia and Ting Chen
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics (2009) 25 (19): 2514-2521.

Pindel 0.2.5b8 – INDEL (insertions and deletions) Detection

Pindel 0.2.5b8

:: DESCRIPTION

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

::DEVELOPER

The Genome Institute at Washington University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Pindel

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Nov 1;25(21):2865-71. Epub 2009 Jun 26.
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

COSMID – CRISPR Search with Mismatches, Insertions and/or Deletions

COSMID

:: DESCRIPTION

COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions) is a web-based tool that searches genomes for potential off-target sites (http://crispr.bme.gatech.edu).

::DEVELOPER

Peng Qiu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Cradick TJ, Qiu P, Lee CM, Fine EJ, Bao G.
COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites.
Mol Ther Nucleic Acids. 2014 Dec 2;3(12):e214. doi: 10.1038/mtna.2014.64. PMID: 25462530; PMCID: PMC4272406.

SoloDel 1.0.0 – Somatic Low-frequent Deletion Caller Model

SoloDel 1.0.0

:: DESCRIPTION

SoloDel is a Java based somatic deletion caller designed for whole-genome sequencing data from unmatched samples. SoloDel is specialized for identifying somatic deletions with frequently existing sampling issues : low mutational frequency in cell population and absence of the matched control samples.

::DEVELOPER

SoloDel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 SoloDel

:: MORE INFORMATION

Citation

SoloDel: A probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data.
Kim J, Kim S, Nam H, Kim S, Lee D.
Bioinformatics. 2015 Jun 11. pii: btv358.

InDelFixer 1.1 – An Insertion and Deletion Fixing Aligner for 454, Illumina and PacBio

InDelFixer 1.1

:: DESCRIPTION

InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 InDelFixer

:: MORE INFORMATION

ICC 2.0.1 – Insertion, Deletion and Carry-forward Error Correction for Next-generation Sequencing

ICC 2.0.1

:: DESCRIPTION

ICC (Indel and Carryforward Correction) is a software pipeline to analyze 454 pyrosequencing data, including read quality filtering and alignment, indel and carryforward error correction, single nucleotide variant calling, and calculation of nucleotide variant and hyplotype frequencies.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 ICC

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 1;29(19):2402-9. doi: 10.1093/bioinformatics/btt434. Epub 2013 Jul 29.
Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.
Deng W1, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI.