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.
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.
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.
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.
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).
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.
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.