Stampy pipeline

Stampy specifications

Information


Unique identifier OMICS_00691
Name Stampy
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data FASTQ,FASTA,GZIPPED,SAM,BAM
Output data SAM
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 1.0.20
Stability Stable
Registration required Yes
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Gerton Lunter <>

Additional information


http://www.well.ox.ac.uk/~gerton/README.txt

Publication for Stampy

Stampy citations

 (10)
2018
PMCID: 5755140

[…] further filtered with trimmomatic [17] for low quality leading/trailing bases with phred quality lower than 20. subsequently sequences were aligned to the human reference genome (version hg19) with stampy [18]. additionally, the initial 5 bases were trimmed due to potential allele bias in case of single nucleotide polymorphisms (snp) present in restriction enzyme cutting sites. snps were called […]

2017
PMCID: 5402963

[…] the reference genome s. fleurettii 402567 was used to perform a snp analysis of the predicted core genome of s. sciuri, s. vitulinus and s. fleurettii isolates. snp analysis was performed using stampy (version 1.0.11) where reads were mapped to the reference genome. snp calling was performed using samtools (version 0.1.12), and neighbor joining (nj) analysis was used to assess […]

2017
PMCID: 5408089

[…] for paired- and single-end reads, we randomly selected one read per pair from paired-end data from the original 99 individuals to use for further analysis., all sequence data were mapped using stampy 1.0.21 (lunter and goodson 2011) with default settings to an exon-only reference generated from the capsella rubella reference genome (josephs et al. 2015; slotte et al. 2013). capsella […]

2016
PMCID: 4915495

[…] of the coding exome, as specified by the consensus coding sequence (ccds) project,16 in both individuals. reads were aligned to the human sequence version 37d5 (hs37d5) reference genome using stampy17 and variant calling of single nucleotide variants (snvs) and short insertions and deletions (indels) was undertaken using platypus (v0.5.1).18 analysis of coding variants was undertaken […]

2016
PMCID: 4906373

[…] using standard procedures, captured using the sureselect human all exon kit (agilent technologies), and then sequenced using illumina technology. the 51-bp paired-end reads were mapped using stampy (lunter and goodson, 2011), and duplicate pcr reads were removed using picard (http://picard.sourceforge.net/). single-nucleotide variants were called using platypus (rimmer et al., 2014)., […]

Stampy institution(s)
Wellcome Trust Centre for Human Genetics, Oxford, UK
Stampy funding source(s)
Supported by the Wellcome Trust, grant no. 075491/Z/04.

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