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chevron_left Structural variant detection Read alignment SNP detection Deletion detection Insertion detection Indel detection chevron_right
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Platypus specifications

Information


Unique identifier OMICS_00068
Name Platypus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Cython, Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Platypus

Platypus in pipelines

 (13)
2018
PMCID: 5807544
PMID: 29426844
DOI: 10.1038/s41598-018-20783-6

[…] the populus trichocarpa reference genome v.3.0 using bwa v0.7.13, together with samtools v0.1.19 to produce an alignment file for each individual tree. haplotype variants were then called with platypus v0.8.1 and filtered using the r package stackr v0.5.3. eleven more individuals that yielded doubtful results were removed from the data set, leaving 309 individuals for genetic data […]

2018
PMCID: 5896245
PMID: 29634948
DOI: 10.1016/j.ccell.2018.03.013

[…] 'complete'), defining each genotype value as follows:(i)homozygous 1/1: 0(ii)heterozygous 1/2: 0.5(iii)homozygous 2/2: 1, homozygous 1/1: 0, heterozygous 1/2: 0.5, homozygous 2/2: 1, we used platypus version 0.8.1 for detecting and genotyping single nucleotide variants (snvs) and small insertions and deletions (indels) (). variants were ascertained from the high-coverage genomes […]

2017
PMCID: 5411691
PMID: 28487883
DOI: 10.1101/mcs.a001610

[…] mpileup and bcftools () version 0.1.19 with parameter adjustments to allow calling of somatic variants with low allele frequency using heuristic filtering as described previously (). we applied platypus () version 0.7.4 to identify short indels with a similar reliability scoring as for snvs. after not detecting any coding indels with the default high-confidence threshold of 8, the value […]

2017
PMCID: 5439955
PMID: 28542371
DOI: 10.1371/journal.pone.0178169

[…] small indels and multiple nucleotide variations (mnv) located near or within exons were called by both algorithms, while indel calls made by a single algorithm (3 indels by mutect2 and 19 indels by platypus) were visualized in igv and confirmed to be false positives. no single variant was shared across tumors and no known selfish or oncogenic mutations were identified (). overall, an average […]

2017
PMCID: 5477361
PMID: 28327575
DOI: 10.1038/ejhg.2017.32

[…] variant calling software. therefore, data from three families where bam files were available in ega were re-analysed with an analysis pipeline that combined multi-sample variant calling with platypus and variant prioritisation using ingenuity variant analysis (www.ingenuity.com/products/variant-analysis), similar to that described previously. for three families where bam files […]


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Platypus in publications

 (46)
PMCID: 5945671
PMID: 29748622
DOI: 10.1038/s41598-018-25544-z

[…] as of february 2016), dbsnp (build 147), 1000 genomes and evs (exome variant server, nhlbi go exome sequencing project (esp), seattle, wa [version esp6500si-v2]) data. indels were identified with platypus callvariants (version 0.8.1, parameter settings genindels = 1, gensnps = 1, buffersize = 100000 and maxreads = 10000000). all indels were annotated using annovar (version as of november […]

PMCID: 5913675
PMID: 29688544
DOI: 10.1093/molbev/msy041

[…] c. martin, elizabeth m. batty, and julie hussin contributed equally to this work., the platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. despite widespread interest in its unusual biology, little is known […]

PMCID: 5807544
PMID: 29426844
DOI: 10.1038/s41598-018-20783-6

[…] the populus trichocarpa reference genome v.3.0 using bwa v0.7.13, together with samtools v0.1.19 to produce an alignment file for each individual tree. haplotype variants were then called with platypus v0.8.1 and filtered using the r package stackr v0.5.3. eleven more individuals that yielded doubtful results were removed from the data set, leaving 309 individuals for genetic data […]

PMCID: 5805678
PMID: 29422656
DOI: 10.1038/s41467-018-03025-1

[…] marked with sambamba version 0.6.5. single-nucleotide variations (snvs) and insertions/deletions (indels) were called using an in-house workflow, based on samtools/bcftools 0.1.19 (for snvs) and platypus 0.8.1 (for indels),. the annotation was performed with annovar (version 2016feb01). to remove artifact snvs/indels we calculated a ‘confidence score’ for each mutation. this score was first […]

PMCID: 5761188
PMID: 29316957
DOI: 10.1186/s13058-017-0929-z

[…] score recalibration and indel realignment performed using the genome analysis toolkit (gatk v3.2.2) []. gatk unifiedgenotyper v2.4 (broad institute, cambridge, ma, usa) [], haplotypecaller [] and platypus [] were used for variant calling. annotation of variants was performed using a local copy of the ensembl [] version r73 database and a customised version of ensembl variant effect predictor. […]


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Platypus institution(s)
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK

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