mmolari/kitp_qbio_bootcamp

Part of the tutorials for the kitp qbio school bioinformatics bootcamp

Bioinformatic bootcamp notes - read alignment to reference

This small repository contains notes for the bioinformatics bootcamp of the Qbio course, in occasion of the 2024 KITP program Horizontal Gene Transfer and Mobile Elements in Microbial Ecology and Evolution

They cover the topic of aligning reads to a reference. We consider the example of a dataset obtained by Nanopore sequencing a phage isolate. The tutorial is divided in three sections:

• a look into the fastq file
• aligning to a reference
• inspecting alignments with IGV

setup

Get the required software by:

• installing samtools and minimap2 using conda or mamba:

  conda create -n aln_env -c bioconda -c conda-forge minimap2 samtools

  remeber to activate the environment before using the tools!
• download IGV.

you should have in your folder:

• the fast file reads.fq containing the reads
• the reference sequence bas54.fa, corresponding to phage Bas54 from the Basel collection.