TAREAN

Tandem repeats Galaxy CLI

Reconstructs satellite repeat consensus sequences from RepeatExplorer2 read clusters

Reconstructs the monomer sequence of satellite repeats from RepeatExplorer2 read clusters. It resolves the consensus from k-mer frequencies within a cluster rather than from an assembly, which works even when the array itself cannot be assembled.

Output

Consensus monomer sequences for the satellites found
A confidence category per satellite, separating well-supported reconstructions from tentative ones
Cluster-level reports and k-mer based diagnostics

TAREAN at a glance

Input

sequencing reads

Run it on Galaxy

RepeatExplorer Galaxy server, in a browser, no installation needed

Run it on the command line

Also available as a command-line program. See the repository for installation and usage.

Protocol

Published RepeatExplorer2 protocols

Documentation

Repository and README

Used together with

RepeatExplorer2

How to cite

Novák P., Ávila Robledillo L., Koblížková A., Vrbová I., Neumann P., Macas J. (2017) TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Research 45: e111-e111. doi:10.1093/nar/gkx257