Small non-coding RNAs (sRNA/sncRNAs) are generated from different genome locus and have revealed playing important roles in biological process, such as cell proliferation, priming of viral reverse transcriptases, regulation of gene expression, RNA processing. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify sRNAs and there are many tools have been developed to analysis sRNAs. However, to the best of our knowledge, most of available tools pay the main attention to study miRNA and related function. The comprehensive web-based tool to bench analysis other diverse kind of sRNAs and their potential function is still lacking. Besides, many small RNAs, such as tRF, rRNA derived sRNA, and even miRNA, contain diverse kind of RNA modifications. The highly repetitive elements content in these small RNAs impede the identification of sRNA modification based on conventional immunoprecipitation methods, such as MeRIP-Seq. The chemical cleavage based modification calling method has been developed recently and showed high efficiency based on cleavage identification. In this study, a novel web server sRNAtools is presented, which can be used to discovery, profile and functional annotate diverse kind of sRNAs (including miRNA, piRNA, tRFs, siRNA, snRNA, snoRNA, rRNA, and plant specific 24-nt siRNA, phasiRNA and natsiRNA) which can not only be used in sRNA-Seq, but it is can also be used in single cell sRNA-seq. Beside, sRNA modifications can be identified with site resolution based on cleavage based technology.

sRNAtools have these main features:

• sRNA can be detected and profiled for as many as 21 model species
• Unbiased classify the sRNA into different categories
• Differential expression analysis with group case small RNAs transcriptome
• Gene targets and function prediction for sRNA
• Diverse ways to upload small RNA sequencing data in very interactive queue system
• sRNA modification calling using cleavage-based method
• Local versions based on program package/Docker/VirtureBox are also available
• Very user-friendly web interfaces and convenient data analysis queue system

small non-coding RNA discovery and profiling with sRNAtools based on high-throughput sequencing

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