FusionCatcher
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Application data |
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| Created by | Daniel N |
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| Biological application domain(s) | RNA-seq, Gene structure |
| Principal bioinformatics method(s) | Sequence alignment |
| Technology | Illumina HiSeq/NextSeq/MiSeq/Solexa |
| Maintained? | Yes |
| Input format(s) | FASTQ, (Compressed) FASTQ, SRA |
| Output format(s) | text |
| Software version | 0.99.4d |
| Programming language(s) | Python |
| Licence | GPLv3 |
| Operating system(s) |
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Summary: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq) from diseased samples).
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The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - to be as automatic as possible (i.e. the FusionCatcher will choose automatically the best parameters in order to find candidate fusion genes, e.g. finding automatically the adapters, building the exon-exon junctions automatically based on the length of the input reads, etc.) while providing the best possible detection rate for finding fusion genes.
FusionCatcher has been published here as pre-print: D. Nicorici, M. Satalan, H. Edgren, S. Kangaspeska, A. Murumagi, O. Kallioniemi, S. Virtanen, O. Kilkku, FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data, bioRxiv, Nov. 2014, DOI:10.1101/011650
A list of articles where FusionCatcher has been used can be found here: http://github.com/ndaniel/fusioncatcher/blob/master/doc/MANUAL.md#3---fusioncatcher-in-scientific-articles
Links
References
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