SOAPfuse statistics

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SOAPfuse specifications

Information


Unique identifier OMICS_01357
Name SOAPfuse
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SOAPfuse

SOAPfuse in publications

 (13)
PMCID: 5834868
PMID: 29499655
DOI: 10.1186/s12885-018-4161-8

[…] when the reads were divided into two fragments, only some of them could be aligned. two-segment alignments could be read to the reference genome using the gene fusion-detection doctrines of the soapfuse software program, which can detect gene fusions using span and junction reads []. this basic method includes 1) comparing the reads to the reference genome alignment and the transcripts […]

PMCID: 5683215
PMID: 29132375
DOI: 10.1186/s12864-017-4256-7

[…] (2 × 100 bp) sequencing technology with an illumina hiseq™ 2000 sequencer (the rna-seq test and its results were analyzed by the bgi tech solutions co., ltd. (bgi tech) (bgi, shenzhen, pr china)., soapfuse software was used to filter noise for the original sequencing reads []. raw reads of eight libraries were performed by removing adapter sequences and low-quality reads, higher n rate […]

PMCID: 5636969
PMID: 28906488
DOI: 10.1038/cddis.2017.402

[…] clean reads was aligned to the reference genome and transcriptome using soap2. no more than three mismatches were allowed in the alignment for each read. the fusion gene detection analyzed using the soapfuse software., sixty npc specimens and 20 noncancerous epithelial tissues used in studies of rrm2-c2orf48 expression based on qrt-pcr were collected from the sun yat-sen university cancer center […]

PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] been shown as a valuable source for detecting fusion genes. several tools have been proposed to identify fusion from transcriptomic data such as jaffa, star-fusion, tophat-fusion, fusioncatcher, and soapfuse. in addition to these short-read-based techniques, idp-fusion, and iso-seq methods can analyse long-read rna-seq data to identify fused genes., here we assessed these approaches in detecting […]

PMCID: 5737606
PMID: 28541529
DOI: 10.1093/nar/gkx453

[…] in other published algorithms which prioritize potentially oncogenic events by read count, or by scores that lack an underlying null statistical model. we have tested machete against star-fusion, soapfuse (), as well as ericscript, the best performing algorithms as defined by a recent evaluation (). we have evaluated machete on a simulated negative control dataset () and a ‘mixed’ dataset […]


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