miRPursuit—a pipeline for automated analyses of small RNAs in model and nonmodel plants

Abstract

miRPursuit is a pipeline developed for running end-to-end analyses of high-throughput small RNA (sRNA) sequence data in model and nonmodel plants, from raw data to identified and annotated conserved and novel sequences. It consists of a series of UNIX shell scripts, which connect open-source sRNA analysis software. The involved parameters can be combined with convenient workflow management by users without advanced computational skills. miRPursuit presents several advantages when compared to other tools, including the possibility of processing several sRNA libraries in parallel, thus easily allowing a comparison of the differences in sRNA read accumulation among sRNA libraries. We validate miRPursuit by using datasets from a model plant and discuss its performance with the analysis of sRNAs from non-model species.

Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos

“…The raw sequencing data files were automatically processed by the sRNA analysis pipeline miRPursuit 62 , with the user-defined criteria described as follows: after a standard pre-processing step, reads were firstly filtered excluding those outside the 18–26 nt range and with an absolute abundance lower than 5; secondly, only reads perfectly mapping (0 mismatches) in the genome of Pinus taeda v1.01-masktrim 63 , defined as the Genome + DB, were considered to be candidate reads in following steps. Conserved miRNAs were identified/annotated by comparison with mature miRNAs deposited in miRBase v.21, allowing up to two mismatches 17 .…”

MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode

“…Reads were then processed with the sRNA analysis pipeline miRPursuit 65 . In an initial step, data was filtered to remove t/rRNAs, low complexity reads, reads with an absolute abundance ≤ 5, and reads outside the range of 18–26 nucleotides.…”

Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability

“…Libraries were processed independently using miRPursuit (Chaves, Costa, Rodrigues, Bohn, & Miguel, 2017), an open source tool to automate the management of workloads, based on publicly available tools such as the UEA small RNA workbench (Stocks et al, 2012). The number of occurrences for each different sequence was assigned as total read count value.…”

“…A combined strategy based on miRPursuit (Chaves et al, 2017) and isomiREX (Sablok et al, 2013) was used to de novo identification of all loci/transcripts with potential to form hairpin structures. Canonical miRNAs and miRNA* were associated to each locus/transcript during hairpin identification.…”