Custom Code used for analysis of non-templated nucleotides in Paramecium tetraurelia

A Custom Pipeline analyzing non-templated nucleotides in smallRNA sequencing data.

Base version of the pipeline can be found here: https://github.com/greenjune-ship-it/untemplated-nucleotides-search

This repository here contains a modified version of the snakefile this pipeline uses, realizing the split between sense and antisense mapping reads prior to weblogo creation, as well as an alternative script for weblogo-creation normalizing the base content of reads to the Paramecium tetraurelia genome base composition.

Requirements to run the pipeline:

• cutadapt 2.8 with Python 3.8.10
• bowtie 1.2.3
• samtools 1.10
• graphviz 2.43.0
• seqtk 1.3
• BBMap and default-jre
• GPL Ghostscript 9.50
• weblogo 3.7.8