Gene fusion identification software tools | RNA sequencing data analysis
Gene fusions arising from chromosomal translocations have been implicated in cancer. RNA-seq has the potential to discover such rearrangements generating functional proteins (chimera/fusion). Recently, many methods for chimeras detection have been published.
Assists users in mapping reads to a reference genome. Subread offers a suite of programs for processing next-generation sequencing read data. This package includes Subread (an aligner), Subjunc (an aligner), Sublong (a long-read aligner), Subindel (a long indel detection program), featureCounts (a read quantification program), exactSNP (an SNP calling program) and other utility programs.
Maps short sequencer reads to reference genomes. Segemehl is a read aligner that allows to detect mismatches, insertions and deletions. The software implements a matching strategy based on enhanced suffix arrays (ESA): it aims to find the best-scoring seed for each suffix of a read. The tool lack, which rescues unmapped RNAseq, reads and works in conjunction with segemehl and many other frequently used split-read aligners, is distributed together with it.
Finds fusion events by aligning the relatively short reads from next-generation sequencers. TopHat-Fusion employs unspliced alignment software and finding paired reads that map to either side of a fusion boundary to proceed. It can discover individual reads that span a fusion event and events involving novel splice variants and entirely novel genes. This tool is able to retrieve intra-chromosomal rearrangements while excluding most but not all read-through transcripts.
Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq, MeDIP-seq and ChIP-seq experiments. This tool includes standard differential expression analysis for different experimental conditions, as well as differential splicing analysis. It can notice variants in the transcriptome and gene fusion events.
Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server) differs from standard desktop solutions or open source solutions, with Array Studio providing the graphical user interface for NGS and omic analysis and visualization and Array Server providing the enterprise back-end solution for project management, sample management and data storage.
Serves for the detection of gene fusions from RNA-Seq data. Arriba is a command-line tool specially designed for the use in a clinical setting. This tool can also detect other structural rearrangements with potential clinical relevance, such as exon duplications or truncations of genes.
Allows gene fusion discovery using RNA-Seq data. Defuse’s aim is to guide a dynamic programming-based split read analysis with discordant paired end alignments. The software employs heuristic filters to reduce the number of false positives and produces a fully annotated output for each predicted fusion. It was applied to ovarian tumours and sarcomas from the OvCaRe (Ovarian Cancer Research) frozen tumor bank.