SnowShoes-FTD statistics

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Protocols

SnowShoes-FTD specifications

Information


Unique identifier OMICS_01356
Name SnowShoes-FTD
Alternative name SnowShoes-Fusion Transcript Detection
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Yan W. Asmann
  • person_outline Aubrey Thompson

Additional information


http://www.mayo.edu/research/departments-divisions/department-health-sciences-research/division-biomedical-statistics-informatics/software/bioinformatics-software-packages

Publication for SnowShoes-Fusion Transcript Detection

SnowShoes-FTD citations

 (7)
call_split

Recurrent rearrangements of the Myb/SANT like DNA binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma

2017
PLoS One
PMCID: 5315303
PMID: 28212443
DOI: 10.1371/journal.pone.0171265
call_split See protocol

[…] sequencing reads. For discovery of gene fusions, evidenced by paired reads mapping to two different genes, and/or reads spanning predicted fusion junctions, we used Chimeriscan [], TopHat-Fusion [], SnowShoes-FTD [], and deFuse [] software. RNA-seq reads are available at GEO (accession GSE76354). Analysis of publically-available The Cancer Genome Atlas (TCGA) RNA-seq data was done using Wanderer […]

library_books

Recurrent hormone binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth

2016
Sci Rep
PMCID: 4861919
PMID: 27160768
DOI: 10.1038/srep25521

[…] rences. P-values < 0.05 were considered statistically significant. Paired-end RNA-seq fusion transcript analysis of TCGA RNA-sequencing data from 295 tumors to detect mRNA fusions was performed using SnowShoes-FTD as described earlier. Parameters used to define a fusion transcript of high confidence were at least two unique fusion junction spanning split reads within the dataset and at least five […]

library_books

Transcriptome Profiling of Pediatric Core Binding Factor AML

2015
PLoS One
PMCID: 4580636
PMID: 26397705
DOI: 10.1371/journal.pone.0138782

[…] e events[, –]. Most detection methods, however, have proved problematic because of high false-positive rates[, ]. We used four gene-fusion detection methods—Defuse[], Tophat-Fusion[], FusionMap[] and Snowshoes-FTD[] to identify gene-fusion events in our pediatric AML samples. The number of putative fusion events identified ranged from 300 to more than 2000 for each detection method, while only a f […]

library_books

Common Oncogene Mutations and Novel SND1 BRAF Transcript Fusion in Lung Adenocarcinoma from Never Smokers

2015
Sci Rep
PMCID: 4434945
PMID: 25985019
DOI: 10.1038/srep09755

[…] 000 instrument with a 50 cycles pair-end read. FASTQ formatted raw files for each sample were mapped and aligned in reference to hg19. Fusion transcripts were identified as previously described using SnowShoes-FTD version 2.0. A fusion was called when there were at least two reads that span the fusion junction and three reads that encompassing the two fusion transcripts. Candidate fusion transcrip […]

call_split

Open access synthetic spike in mRNA seq data for cancer gene fusions

2014
BMC Genomics
PMCID: 4190330
PMID: 25266161
DOI: 10.1186/1471-2164-15-824
call_split See protocol

[…] y read quality assessment using FASTQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We analyzed the data using three fusion detection tools: ChimeraScan [], Tophat-Fusion [], and Snowshoes-FTD [] (hereafter referred as CHS, THF, and SSH respectively). The command-line parameters are described in Figure . For each analysis tool, we captured the number of sequencing reads suppor […]

library_books

Fusion Transcript Discovery in Formalin Fixed Paraffin Embedded Human Breast Cancer Tissues Reveals a Link to Tumor Progression

2014
PLoS One
PMCID: 3984112
PMID: 24727804
DOI: 10.1371/journal.pone.0094202

[…] locations has been facilitated by the application of RNA-Seq technologies. Numerous bioinformatics methods are available to detect fusion transcripts from RNA-Seq paired-end read data (ChimeranScan , SnowShoes-FTD , GSTRUCT-fusions and GFP ) or single-end read (TopHat-Fusion , FusionMap and FusionFinder ). All fusion transcript detection methods utilize split reads, in which a single-end read or […]

Citations

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SnowShoes-FTD institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA; Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL, USA; Illumina Inc., Hayward, CA, USA; Department of Medicine, Mayo Clinic, Jacksonville, FL, USA
SnowShoes-FTD funding source(s)
Supported by 26.2 with Donna Foundation; Bankhead Coley program of the State of Florida (10-BG012-1); Mayo Foundation and the Mayo Clinic Comprehensive Cancer Center (CA151160); by a generous gift from James and Donna Barksdale.

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