:: 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
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: 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.
:: DESCRIPTION
ExonDel is a tool designed specially to efficiently detect exon deletions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: DOWNLOAD
:: 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.