LongOmics Project

Major Research Project - Master Bioinformatics and Systems Biology, Vrije Universiteit Amsterdam

The interactive application (streamlit_app.py) has been developed within the Long-omics project. It provides functionalities to get insights about Nanopore Long Read samples.

Files needed for the application:

• depth_LRS_ID.tsv: TSV file with coverage information. Three columns: chromosome, genomic location and count.
• merged_LRS_IS.csv: Merged VCF files (merged_LRS_ID.csv), that are the output of the Variant Calling tools in VCF format, merged with the pyhton script merge_vcf.py.
• sample_info.csv provides information about all the samples included in the study. The row names are the samples id (LRS_id). More in detail, it requires the following columns: Chr, Start, End, Length, Gene, Method (Adaptive Sampling / Cas9 Enrichment).

Snakemake scripts:

• preprocessing.smk: alignment and preprocessing of fastq files with minimap2 and bedtools.
• VC.smk: variant calling with SVIM, Sniffles2, CuteSV and Pepper.
• vep.smk and annotsv.smk: VEP and AnnotSV to assess relevance of the variants identified by the variant callers.