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SHI7 (SHort-read Iterative Trimmer) for Linux, Mac, and Windows (WSL)
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@GabeAl GabeAl released this 05 Sep 23:07
· 185 commits to master since this release
v0.91f
f295c2b

Changes

  • Updated some default parameters for trimming
  • Fixed wording of some help strings
  • Added new "drop_r2" option to skip outputting R2's when present (but still use them for adapter detection)
  • Some code changes (T/F dictionary handling)
  • Miscellaneous bugfixes (removing multiple "R1" strings in sample name, non-final R1's)
  • Tried to make binaries executable by default within the zip file (potentially saving the 'chmod +x' step -- testing needed)

Installation instructions:

Extract to a directory in your executable PATH (or anywhere, and add that directory to PATH). Windows users, use the "linux" package in the WSL environment (compatible with Windows 10 Creator's update and later).

Use by calling shi7.py anywhere.

Cite

Please cite SHI7 like so:
Al-Ghalith GA, Ang K, Hillmann B, Knights D. (2017). SHI7: A Streamlined short-read iterative trimming pipeline. DOI:10.5281/zenodo.885570 DOI

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