Mirge3

This release supports Python3 and has improved performance along with advanced graphics with additional features for processing small RNA data.

[](https://sourceforge.net/projects/mirge3/files/v3.0.0/mirge3-0.0.1.tar.gz/download)

- Edited parallel processing to use memory view object and send chunks of memory for processing parallely instead of bunch of reads. This runs more efficiently in terms of speed and memory usage (Major update).
- Added link to Biocontainers in the readme as a badge and provided the link in the installation page of the documentation.
- Added checkpoints for resume function to verify the availability of input files.
- Corrected the column order of the differentiall expression results files. Also, added checkpoint to install packages ggplot2 and DESeq2 if not already installed in a new library path.
- Corrected checkpoint to Include bowtie version 1.0.0

- Added exception handling to use correct adapter parser function for any installed version of cutadapt based on recent [GitHub issue](https://github.com/mhalushka/miRge3.0/issues/45#issuecomment-1311958554).
- Rest of the features are same as v0.1.0.

- Corrected Cutadapt version fixes in libs/digest.py and updated the check for bioconda installation compatability,
- Rest of the features are same as v0.1.0.

- Introduced new feature and updated user guide for "[Save and resume functions](https://mirge3.readthedocs.io/en/latest/quick_start.html#save-and-resume-functions)"
- Updated user guide for "[Trimming both 5’ and 3’ adapters - Linked adapters](https://mirge3.readthedocs.io/en/latest/quick_start.html#trimming-both-5-and-3-adapters-linked-adapters) "
- Introduced "[Frequently asked questions (FAQ)](https://mirge3.readthedocs.io/en/latest/faqs.html)" in documentation and described how to reach out
- Introduced a fix for the recent [issue](https://github.com/mhalushka/miRge3.0/issues/45#issue-1273542412) "`Parser.py missing AdapterParser in cutadapt`"
- Introduced a QC/check for essential files in the library and its path prior to the execution of miRge3.0 on the input samples
- Corrected SAM flag denoting negative strand reads
- Added print statement to display the path of the output folder upon successful completion of miRge3.0 execution
- Introduced threshold feature for miRNA error correction package (miREC feature)

- Updated MANIFEST.in file to include miREC package