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Citations per year

Number of citations per year for the bioinformatics software tool ShortStack

Tool usage distribution map

This map represents all the scientific publications referring to ShortStack per scientific context
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ShortStack specifications


Unique identifier OMICS_00384
Name ShortStack
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for ShortStack

ShortStack citations


Paramutation like features of multiple natural epialleles in tomato

BMC Genomics
PMCID: 5859443
PMID: 29554868
DOI: 10.1186/s12864-018-4590-4

[…] in the GEO data set.To find differential sRNA loci between M82 and ILs, sRNA libraries from IL1–1, IL2–5, IL8–3 and two M82 seedlings (from []) were mapped and clustered on Heinz genome SL2.50 using ShortStack v3.3.3 [] with default parameters. sRNA counts on the defined loci were analysed with DESeq2 v1.8.1 []. […]


Genome re annotation of the wild strawberry Fragaria vesca using extensive Illumina and SMRT based RNA seq datasets

PMCID: 5824900
PMID: 29036429
DOI: 10.1093/dnares/dsx038

[…] the 3′ adapters were trimmed off using Cutadapt. Then, the resulting .fasta file was mapped against the Fvb genome using bowtie (version 0.12.8) with following parameters: -q -v 0 -p 30 -S -a -m 50. ShortStack was subsequently employed to identify small RNA clusters, and only the dominant 20- to 24- nt in length and DCL-derived small RNA loci (more possibly related to RNAi) called out by ShortSta […]


Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases

PMCID: 5615367
PMID: 28925938
DOI: 10.3390/genes8090234

[…] NGS approaches, downstream data analysis might be performed using different tools: small RNA toolkit [], miRDeep [] and miRDeep2 [], miRanalyzer [,], SeqBuster [], DARIO [] UEA sRNA workbench [] and ShortStack []. In certain cases, some of these tools include other prediction tools for novel microRNAs or isoforms of miRNAs (isomiRs) quantification. However, they do not generally offer functional […]


Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination

Genome Biol
PMCID: 5599894
PMID: 28911330
DOI: 10.1186/s13059-017-1302-3

[…] Small RNA-seq reads were trimmed with trimgalore (v0.4.2) and sequences of 18–24 nt in length were mapped and clustered onto the Arabidopsis TAIR10 genome with ShortStack v3.6 []. The read counts on all 87,000 defined clusters were subjected to differential analysis with DESeq2 v1.10.1 []. Small RNA loci were considered to vary during the time course when th […]


The use of high throughput small RNA sequencing reveals differentially expressed microRNAs in response to aster yellows phytoplasma infection in Vitis vinifera cv. ‘Chardonnay’

PLoS One
PMCID: 5558978
PMID: 28813447
DOI: 10.1371/journal.pone.0182629

[…] ns, sRNA library files of the 18 to 26 nt reads, from all six libraries, were grouped into a single file that served as input for sRNAbench v0.9 [] (, and Shortstack v0.4.1 [], using the default parameters of the respective packages. sRNAbench was also used for the discovery of sequence variants of known miRNAs, also known as miRNA isoforms (isomiRs). T […]


Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs

PMCID: 5545994
PMID: 28786034
DOI: 10.1186/s12284-017-0177-y

[…] RNA database) (Griffiths-Jones et al., ) and PLncDB (plant long non-coding RNA database) (Jin et al., ) are useful to check whether the sRNA is originated from a miRNA precursor or a lncRNA. Besides, ShortStack should be a useful tool to analyze the sRNA-seq data based on the available reference genomes (Axtell, ) (Table ). It can output reports showing sRNA size distributions, repetitiveness, hai […]

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ShortStack institution(s)
Department of Biology, and Huck Institutes of the Life Sciences, Penn State University, University Park, PA, USA

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