A web server for interactive analysis and a set of scripts and modules for small RNA-seq, short total RNA-seq, miRNA-seq, single-cell small RNA-seq data processing, analysis, annotation, visualization, and comparison against reference ENCODE and DASHR datasets across >180 human tissues/cell types.

SPAR web server: https://www.lisanwanglab.org/SPAR

SPAR repository with the scripts (command line interface): https://bitbucket.org/account/user/wanglab-upenn/projects/SPAR

Distinctive key features:

• Ab initio (annotation-free) small non-coding RNA (sncRNA) discovery and characterization across all major small RNA classes (miRNA, piRNA, snoRNAs, scRNAs, snRNAs, tRNAs, tRFs) and novel small RNA loci.
• Expression comparison of user data with >180 reference human tissues, cell types and cell lines from DASHR and ENCODE
• Annotations for GRCh37/hg19, GRCh38/hg38, and mm10 references genomes
• Interactive sncRNA expression/annotation table for data exploration
• Analyze public small RNA datasets https://www.lisanwanglab.org/SPAR/analyze-public-dataset

• Analyze your own small RNA data https://www.lisanwanglab.org/SPAR/analyze-own-data

  Supported file formats:

• raw sequencing reads (FASTQ)

• mapped reads (BAM)

• genome-wide coverage tracks (BigWig)

  Supported sequencing protocols:

• small RNA-seq

• miRNA-seq
• short total RNA-seq

• single cell small RNA-seq

  Citation: SPAR has been published in Nucleic Acids Research.

Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung. SPAR: small RNA-seq portal for analysis of sequencing experiments. NAR 2018 (Web Server issue). https://doi.org/10.1093/nar/gky330