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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 No

Versioning


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Additional information


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

Publication for Stampy

Stampy in pipelines

 (28)
2018
PMCID: 5755140
PMID: 29301499
DOI: 10.1186/s12885-017-3943-8

[…] further filtered with trimmomatic [] 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 []. 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: 5408089
PMID: 28402527
DOI: 10.1093/gbe/evx068

[…] curacy 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 () with default settings to an exon-only reference generated from the capsella rubella reference genome (; ). capsella rubella and c. grandiflora diverged between 50,000 and 100,000 year […]

2017
PMCID: 5430854
PMID: 28455506
DOI: 10.1038/s41598-017-01133-4

[…] ii dna library prep kit (new england biolabs) and sequenced on the miseq platform as described in de vries et al.. reads were mapped to the m1cam reference genome (accession no. cp012149) using stampy, variants were identified with samtools and the effect at the protein level was predicted using snpeff. deletion mutants in pfla and flad were analysed previously., a tn donor plasmid suitable […]

2017
PMCID: 5483921
PMID: 28468851
DOI: 10.1128/JCM.00363-17

[…] described () from a single colony subcultured on cba and incubated for 18 to 24 h. sequencing was performed using the illumina hiseq or miseq platforms., for all outbreaks, reads were aligned using stampy v1.0.17 to a standard reference genome (mrsa252; genbank no. nc_002952) (). six outbreaks were also mapped to clonal complex-specific reference genomes obtained from in-house collections […]

2017
PMCID: 5924597
PMID: 29091079
DOI: 10.1038/mi.2017.74

[…] were paired end sequenced and sequenced to an average coverage between 27 and 40 quality reads per base. resulting 100 base pair reads were mapped to the grch37d5/hg19 human reference sequence using stampy and the snvs and short indels were called with platypus. variant files were analyzed using qiagen’s ingenuity® variant analysis™ software (www.qiagen.com/ingenuity, qiagen redwood city). high […]


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Stampy in publications

 (209)
PMCID: 5930307
PMID: 29717015
DOI: 10.1128/mBio.00736-17

[…] according to their barcodes and mapped to the genome sequence of the reference genome salmonella enterica subsp. enterica serovar typhimurium lt2 (genbank accession number ae006468.2) using stampy (). for differential gene expression analysis, the r package deseq () was employed. differentially expressed genes were identified using the nbinomtest function based on the negative binomial […]

PMCID: 5945548
PMID: 29755658
DOI: 10.18632/oncotarget.24872

[…] hiseq2000 technology (illumina, united states). paired end fastq files were extracted using casava software (v.1.8.1, illumina) and aligned to build 37 (hg19) of the human reference genome using stampy and bwa software [, ]. alignments were processed using the genome analysis tool kit (gatk) pipeline []. we imposed gatk internal calling thresholds and required a genotyping quality (gq) of ≥ […]

PMCID: 5885015
PMID: 29557774
DOI: 10.1099/mgen.0.000163

[…] raw data. at each step, read quality was assessed with fastqc (version 0.10.1) []. single-end reads were aligned to the m. bovis af2122/97 or m. tuberculosis h37rv reference genomes with the aligner stampy in hybrid mode with the bwa algorithm []. read counts for each gene were calculated using featurecounts, set to unambiguously assign uniquely aligned single-end reads in a stranded manner […]

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

[…] dovetail hi-c scaffolding (bioproject reference prjna433451; genbank accession gca_002966995.1), which we will call ornana3 here., we mapped the paired-end data from all 58 samples to ornana3 using stampy () without bwa premapping. duplicates were removed using picard markduplicates tool (http://broadinstitute.github.io/picard). variant calling was performed jointly on the 58 samples using […]

PMCID: 5800051
PMID: 29402214
DOI: 10.1186/s12864-018-4490-7

[…] alignments were graphically represented using 1) mummerplot and 2) gevo (https://genomevolution.org/coge/gevo.pl). second, a subset of f2 illumina paired-end reads (40x) was aligned to f2 wga using stampy and a 24x depth f2 illumina mate-pair reads (3 kb) was aligned to f2 wga using smalt 0.7.4 (http://www.sanger.ac.uk/science/tools/smalt-0), which aligns independently each read of a pair. […]


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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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