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SPLITREAD specifications


Unique identifier OMICS_00323
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.1
Stability Stable
Maintained Yes



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Publication for SPLITREAD

SPLITREAD in publications

PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] split-read algorithm successfully identified large indels. other computational tools developed after pindel still utilize this algorithm as the foundation in their methods for detecting indels., splitread [] was developed to specifically identify structural variants and indels in wes data from 1 bp to 1 mbp building on the split-read approach of pindel []. the algorithms used by samtools […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] is particularly well-tuned for the investigation of insertions and deletions of 50–100 bp., though sr methods were conceived for sanger sequencing reads (mills et al., ), algorithms such as pindel, splitread, and gustaf (ye et al., ; karakoc et al., ; trappe et al., ) use paired-end ngs reads to identify svs (or indel) events. sr approaches take advantage of one-end anchored reads, namely […]

PMCID: 4379406
PMID: 25556237
DOI: 10.1093/molbev/msu405

[…] sequences also verified the accuracy of our observation for one human deletion that we found to be deleted in denisovan, but not in altai neandertal genome., last but not least, we used the software splitread (http://splitread.sourceforge.net/, last accessed december 10, 2014) to remap neandertal and denisovan reads to junctions of the deletion breakpoints as defined in 1kg deletion data set […]

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SPLITREAD institution(s)
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
SPLITREAD funding source(s)
Supported by a Simons Foundation Autism Research Initiative Award SFARI191889 and National Institutes of Health grants HD065285, HHSN273200800010C, HL 102926.


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