snpkit Beta 2.0.1

• Converting naked python scripts to executable

snpkit Beta 2.0

Major changes in python code:

• Moving base python code to NumPY/Pandas way of analyzing SNP/Index Matrices.
• Migrated Python2 to Python3
• Loading and Analyzing temporary files in system tmp folder for faster processing.
• GATK3 to GATK4 migration.
• Beta Matrix version - Adding Eggnog and SIFT annotations to Matrices.
• Minimal print messages.

Integrated Great Lakes SLURM into the pipeline.

First Stable Release - Integrated Great Lakes SLURM into the pipeline.

variant_calling_pipeline

Backing up the code before a new release with great lakes SLURM integration

Backing up the code before a new release with great lakes SLURM integration

1.2.6.1

Making changes to Barplot code - excludeing Phage positions

variant_calling_pipeline

Backing up the code before a new release

variant_calling_pipeline

Backing up the code before a new release

variant_calling_pipeline

• Integrating GATK Indel calling to the pipeline.
• Major changes to SNP/Indel Matrix format.

variant_calling_pipeline 1.2.2

Merge branch 'master' of https://github.com/alipirani88/variant_calli…

variant_calling_pipeline 1.2.1

version 1.2 with new features