Releases: knights-lab/shi7
SHI7: SHort-read Iterative Trimmer with Learning Module
What
Prepared SHI7 for conda installation.
Functionally, this release is identical to 0.9.2, but it adds conda installation support and dynamic version string support for release management.
Please cite this article if you use SHI7:
SHI7: SHort-read Iterative Trimmer with Learning Module
SHI7 with learning module pre-release! Big changes include:
- new shi7_learning.py tries to predict the optimal QC parameters (adaptors, stitching, quality bounds, amplicon/shotgun adjustment...)
- shi7.py has a bunch of fixes too (helps with name corruption)
Changes in 0.92a (Learning module):
- Reduced stringency of paired-end matching detection
- Merged read length counting into subsampled write
- Tweaked trimming quality calculation (more conservative)
- Now uses 1000 instead of 100 reads per sample (more accurate)
- Some tweaks to single-end quality trimming
SHI7 (SHort-read Iterative Trimmer) for Linux, Mac, and Windows (WSL)
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
SHI7 (SHort-read Iterative Trimmer) for Linux, Mac, and Windows (WSL)
Changes
- Fixed some wording in the options and output logs
- Changed defaults for trimming (now stricter)
- Changed defaults for stitching (now allows as little as 10 bases of overlap)
- Added '-outies' shorthand (use as
-outies ffor instance) - Increased aggressiveness of trimming in palindrome (paired end) mode when safe
- Now has a DOI for citation purposes
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
SHI7 for Linux, Mac, and Windows (WSL); all-in-one package
Changes
- Fixed some wording in the options and output logs
- Changed defaults for trimming (now stricter)
- Changed defaults for stitching (now allows as little as 10 bases of overlap)
- Added '-outies' shorthand (use as
-outies ffor instance) - Increased aggressiveness of trimming in palindrome (paired end) mode when safe
- Now has a DOI for citation purposes
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.808832
SHI7 for Linux and Mac; all-in-one package
- Incorporated filename sanitization changes
- Amended license
- Added mac version
- [0.91b] Made flash static
- [0.91c] More robust FASTQ parser
Installation instructions:
- Extract to a directory in PATH (or anywhere, and add that directory to PATH)
- Use by calling shi7.py anywhere
SHI7 for Linux; all-in-one package
Instructions:
- extract in a folder you want the binaries to live
- add that folder to your path
Use shi7.py as normal