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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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