Training: Read Alignments

Aligning sequence reads against a reference sequence is a common process which is utilised in the majority of NGS analyses. This module introduces the concepts surrounding read alignment, some commonly used read aligners, alignment file formats, obtaining statistics on mapped reads and filtering read alignments.

After completing this module, participants will be able to:

• Carry out alignment of NGS reads against reference genome and transcriptome sequences
• Understand the structure of SAM/BAM files
• Sort and index BAM files
• Assign read-groups to BAM files
• Obtain metrics on alignments using samtools and picard
• Filter read alignments using samtools
• Mark duplicate reads in BAM files
• Visualise alignments using a genome browser

• Introduction to Linux
• The HPC Cluster
• Introduction to NGS

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