Please see PHASIS wiki for details on installation, usage, output files and more.
version: v3
release: https://github.com/atulkakrana/PHASIS/releases
updated: 03/10/2017
citation: Preprint-Copy
PHASIS (PHAS Inspection Suite) is a parallelized suite that provides an integrated solution for the large-scale survey of tens to hundreds of sRNA libraries for the following applications: a) de novo discovery of PHAS loci and precursor transcripts, b) a summarization of PHAS loci from specific groups of sRNA libraries, c) a comparison of PHAS summaries between groups corresponding to samples from different stages, tissues and treatments, d) quantification and annotations of PHAS loci, and e) discovery of their miRNA triggers. PHASIS generates easily parsed output files for downstream bioinformatics analysis, formatted result files for immediate consumption and organized ancillary data to facilitate optimizations like a re-summarization to exclude or include libraries. The three PHASIS components are:
1. phasdetect: Identifies library-specific phased-loci
2. phasmerge: Summarizes the libraries-specific results to a non-overlapping genome- or transcriptome-level set, comapares PHAS summaries between groups and annotates PHAS loci
3. phastrigs: Predicts miRNAs triggers for PHAS locus using sPARTA miRNA-target predictions. If supplied with PARE/Degradome data then data supported triggers are reported
Authors:
Atul kakrana
kakrana@udel.edu
Pingchuan Li
lipingchuan@gmail.com