REPOSITORY CURRENTLY UPDATING

Master thesis repository

"Genotyping By Sequencing (GBS) for population genetics and phylogenetics studies of non-model plants: the case of Campanula thyrsoides, and others"

Flavia Leotta (MSc candidate),

Carla Lambertini (Associate Professor, University of Milan),

Chiara Paleni (Post-Doc, Fondazione Human Technopole)

This repository contains the supporting files of my MSc thesis in Bioinformatics. Not only the final .pdf file can be found, but more material can be accessed through the following directories:

"/logs"

Contains .log files from the de novo pipeline, namely:

• demulti_log_2nd_batch.log: the .log file of the demultiplexing process of the second sequencing batch of reads;
• filter_summary_1st_batch.txt and filter_summary_2nd_batch.txt: two files summarizing the output of the filtering step (part of preprocessing) for both sequencing batches;
• ustacks_log.log: the .log file of ustacks step in Stacks: denovo_map.pl pipeline;
• summary_reads_count.txt: finally, a file summarizing the count of reads at each step of the pipeline, from preprocessing to catalogue denovo building.

"/multiqc"

"/reports"

"/scripts"

"/supporting_files"