Simple Handler for Error and Adapter Removal
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README.md

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SHEAR: Simple Handler for Error and Adapter Removal

Authors

James B. Pease (https://www.peaselab.github.io)

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 (https://github.com/vsbuffalo/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.

Manual

See the SHEAR manual here: (https://github.com/jbpease/shear/blob/master/shear.pdf)

Requirements

Python 3.x (recommend) or 2.7.x

Optional, but strongly recommended:

Scythe (any version, https://github.com/vsbuffalo/scythe)

License

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 (http://www.gnu.org/licenses/).