A Pipeline NanoTRF as a New Tool for De Novo Satellite DNA Identification in the Raw Nanopore Sequencing Reads of Plant Genomes.High-copy tandemly organized repeats (TRs), or satellite DNA, is an important but still enigmatic component of eukaryotic genomes.  We developed NanoTRF, a new python pipeline for TR repeat identification, characterization and consensus monomer sequence assembly.  In addition, NanoTRF performs annotation of transposable elements (TEs) sequences within or near satDNA arrays, and the information can be used to elucidate how TR-TE co-evolve in the genome.  Moreover, we validated by FISH that the NanoTRF report is useful for the evaluation of TR chromosome organization-clustered or dispersed.  Our findings showed that NanoTRF is a robust method for the de novo identification of satellite repeats in raw Nanopore data without prior read assembly. 
NanoTRF
We developed NanoTRF, a new python pipeline for TR repeat identification, characterization and consensus monomer sequence assembly. 
Python pipeline
Oxford Nanopore sequencing data provide a valuable source of information on TR organization at the single molecule level. 
Oxford Nanopore sequencing data
This new pipeline requires only a raw Nanopore read file from low-depth (&lt;1×) genome sequencing. 
raw Nanopore read file
The program generates an informative html report and figures on TR genome abundance, monomer sequence and monomer length. 
html report
The program generates an informative html report and figures on TR genome abundance, monomer sequence and monomer length. 
figures on TR genome abundance
We developed NanoTRF, a new python pipeline for TR repeat identification, characterization and consensus monomer sequence assembly.  The program generates an informative html report and figures on TR genome abundance, monomer sequence and monomer length. 
monomer sequence