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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




No version available

Additional information


Publication for SPLITREAD

SPLITREAD citations


IMSindel: An accurate intermediate size indel detection tool incorporating de novo assembly and gapped global local alignment with split read analysis

Sci Rep
PMCID: 5884821
PMID: 29618752
DOI: 10.1038/s41598-018-23978-z

[…] been developed to detect these intermediate-size indels. They can mainly be classified into three approaches: (1) realignment based approach (GATK, Scalpel, SV-STAT), (2) split-read approach (PINDEL, Splitread, PRISM), and (3) local assembly approach (SOAPindel). Recently, hybrid approaches that integrate these approaches have also been developed, resulting in more sensitive indel discovery method […]


A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data

Int J Genomics
PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] to 1 Mbp building on the split-read approach of Pindel []. The algorithms used by SAMtools and GATK limit the size of structural variants, with variants greater than 15 bp rarely being identified []. Splitread anchors one end of a read and clusters the unanchored ends to identify size, content, and location of structural variants []. When compared to GATK, Splitread called 70% of the same INDELs b […]


Detection of Genomic Structural Variants from Next Generation Sequencing Data

Front Bioeng Biotechnol
PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] SSAHA2 [Sequence Search and Alignment by Hashing Algorithm, Ning et al. ()], BWA, or Mosaik. It must be stressed that the latest version of Pindel integrates RP to the SR information (Lin et al., ). Splitread searches for clusters of split reads using balanced splits as seeds. Splitread can detect, at least in theory, deletions without size limitation, while for insertions the size spectrum depen […]


The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes

Mol Biol Evol
PMCID: 4379406
PMID: 25556237
DOI: 10.1093/molbev/msu405

[…] than ten deletions in those random regions in both Neandertal and Denisovan genomes, indicating that a false discovery rate is essentially lower than 5% for both genomes.We used a modified version of SPLITREAD approach (http://splitread.sourceforge.net/, last accessed December 10, 2014) to remap the Neandertal and Denisovan reads to the junctions of the breakpoints of deletions as defined in 1KG d […]


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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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