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CandiSSR specifications


Unique identifier OMICS_29174
Name CandiSSR
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Some assembled sequences from a given species or genus.
Input format FASTA
Output data The final result file containing polymorphic SSRs identified, the flanking sequences of identified PolySSRs, which was used for primer designing and Primer pairs designed for each detected PolySSRs.
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 20170602
Stability Stable
MISA, NCBI "Blastall", ClustalW, Primer3, Bioperl packages
Maintained Yes




No version available


  • person_outline Li-Zhi Gao
  • person_outline Hua Xia

Publication for CandiSSR

CandiSSR citations


Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

BMC Genomics
PMCID: 5885378
PMID: 29618324
DOI: 10.1186/s12864-018-4633-x

[…] However, these tools have not yet integrated a computational solution for systematic assessment of SSR polymorphic status, thus the detected SSRs still require manual screening for the polymorphy []. CandiSSR is a new pipeline to detect candidate polymorphic SSRs not only from the transcriptome datasets but also from multiple assembled genome sequences [].In this study, we employed genome skimming […]


Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

Front Plant Sci
PMCID: 5838013
PMID: 29545814
DOI: 10.3389/fpls.2018.00246

[…] southernmost distribution of P. subaequalis to construct the sequencing library, based on the two assembled sequences, we identified a total of 576 candidate polymorphic SSRs by means of the program CandiSSR. In agreement with previous reports from many other plant taxa (Jiao et al., ; Xia et al., ), dinucleotide motifs are found to be the most common in P. subaequalis. A total of 30 designed pri […]


De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

Biotechnol Biofuels
PMCID: 5450047
PMID: 28572841
DOI: 10.1186/s13068-017-0828-7

[…] ] with the default parameters (K = 25 and a minimum transcript length of 200 bp). Clustering of redundant transcripts was performed with 95% identity and a word size of 10 using CD-HIT v4.6.4 []. The CandiSSR pipeline (available at [] was used to identify microsatellite polymorphisms between A. donax unitranscripts and the ecotype-specific leaf t […]


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CandiSSR institution(s)
Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China; University of Chinese Academy of Sciences, Beijing, China
CandiSSR funding source(s)
Supported by Project of Innovation Team of Yunnan Province, the Top Talents Program of Yunnan Province (20080A009), Hundred Oversea Talents Program of Yunnan Province, and Hundred Talents Program of Chinese Academy of Sciences (CAS).

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