The following repository contains all pipelines and scripts I used to analyse milk microbiota composition in sheep and goat breeds. DNA was first extracted from individual milk samples; regions V3-V4 of 16S were amplified using a specific PCR-based technique and the amplicons were sequenced through Illumina NovaSeq. The aim is to obtain OTU (Operational Taxonomic Unit) tables from raw data, and thus to characterize the milk microbiota at a species-level.
See the WIKI for further information!!!
FastQC: it is software primarily used to provide quality control on raw sequence data coming from high-throughput sequencing pipelines.
MultiQC: it allows generating an overall quality report of all raw sequences.
Cutadapt: it finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads.
MICCA: it is one of the pipelines used in microbiota and microbiome analysis.
1.quality_check.sh = Quality check of the raw sequences (see 0.fastqc.sh and 0.multiqc.py for independent use).
2.rename_and_count.sh = Changing raw sample names to new names with a predefined format. Reads for each sample are also counted.
3.remove_primers.sh = Removing primers and adapters from raw sequences.
Support and development: @filippob