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Protocols

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


No version available

Maintainer


This tool is not available anymore.

Additional information


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

Publication for Stampy

Stampy citations

 (179)
call_split

Combined linkage and association analysis of classical Hodgkin lymphoma

2018
Oncotarget
PMCID: 5945548
PMID: 29755658
DOI: 10.18632/oncotarget.24872
call_split See protocol

[…] mina 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 ≥ 3 […]

call_split

Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

2018
Microb Genom
PMCID: 5885015
PMID: 29557774
DOI: 10.1099/mgen.0.000163
call_split See protocol

[…] 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 to ge […]

library_books

Insights into Platypus Population Structure and History from Whole Genome Sequencing

2018
Mol Biol Evol
PMCID: 5913675
PMID: 29688544
DOI: 10.1093/molbev/msy041

[…] 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 the P […]

library_books

Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants

2018
BMC Genomics
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. Compl […]

library_books

A high throughput screen for active human transposable elements

2018
BMC Genomics
PMCID: 5796560
PMID: 29390960
DOI: 10.1186/s12864-018-4485-4

[…] Sequence data generated by TE-enrichment were de-multiplexed and aligned to the human reference genome (hg19) using the Burrows-Wheeler Aligner [] followed by refinement of BWA alignments with Stampy [], sorting of BAM alignments using Samtools sort [], removal of PCR duplicates using the module MarkDuplicates in Picard [] and BAM indexing using Samtools index. […]

library_books

RNA Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

2018
Genetics
PMCID: 5887150
PMID: 29437826
DOI: 10.1534/genetics.117.300567

[…] and H. melpomene references, each time updating the previous reference with homozygous nonreference calls. These reads were mapped with Bowtie2 and then remapped with the divergent alignment software Stampy (). Homozygous nonreference calls (enriched for sites divergent between the in-group and out-group) were made with GATK’s HaplotypeCaller, with the heterozygosity parameter set to the expected […]

Citations

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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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