Simple Handler for Error and Adapter Removal
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.


SHEAR: Simple Handler for Error and Adapter Removal


James B. Pease (

What is SHEAR?

This program removes adapters, trims, and quality-filters Illumina short reads. The program first will automatically find adapters sequences in your reads and remove them using Scythe (, then reads are filtered by length, quality scores, and in the case of highly repetition of sequence. This provides a quick, integrated, and installation-free method to reduce error in your Illumina short reads. You can also skip Scythe and use your own adapter trimmer, but still use SHEAR for all other trimming.

Key features

  • Simultaneous pair trimming and discarding of orphaned reads (i.e. the other pair of a filtered read).
  • Poly-A and Poly-T tail trimming (good for RNA-Seq)
  • Removes dinucleotide repeat reads.
  • Automatically finds adapter sequences from your samples.


See the SHEAR manual here: (


Python 3.x (recommend) or 2.7.x

Optional, but strongly recommended:

Scythe (any version,


This file is part of shear.

shear is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as publihed by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

shear is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Foobar. If not, see (