REAPR 1.0 – Realignment for Prediction of Structural Non-coding RNA

REAPR 1.0

:: DESCRIPTION

The REAPR pipeline performs computational screens for structural non-coding RNA while revealing even strongly structurally misaligned RNAs.

::DEVELOPER

Bonnie Berger

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • python
  • LocARNA
  • RNAz
  • ViennaRNA
  • squid
  • compalignp

:: DOWNLOAD

  REAPR

:: MORE INFORMATION

Citation:

Sebastian Will, Michael Yu, and Bonnie Berger.
Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs.”
Genome Res. 2013 Jun;23(6):1018-27. doi: 10.1101/gr.137091.111.

REAPR 1.0.18 – Genome Assembly Evaluation

REAPR 1.0.18

:: DESCRIPTION

REAPR (Recognising Errors in Assemblies using Paired Reads) is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

::DEVELOPER

REAPR  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 REAPR

:: MORE INFORMATION

Citation:

REAPR: a universal tool for genome assembly evaluation.
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD.
Genome Biol. 2013 May 27;14(5):R47