Genetics and Next Generation Sequencing for Bioinformatics

Explore the DNA structure, including nucleotides, sugar-phosphate backbone, anti-parallel strands, and complementary base pairing (A–T, C–G), and learn how replication creates new DNA copies.

Dna carries instructions to make proteins via transcription, where mrna copies a gene in the nucleus and carries the code to synthesize proteins, guided by promoters.

Explain how transcription produces mRNA and how translation uses codons to assemble amino acids into proteins, highlighting start and stop codons, gene expression, and intron-exon splicing.

Explore how DNA packs into chromosomes, fixed gene locations on 23 chromosomes define a diploid genome with two gene copies, and how sex chromosomes and protein coding genes shape traits.

Explore how genetic variation arises from replication errors and mutations, creating alleles and variants that shape genotypes and phenotypes across individuals.

Explore inheritance patterns in peas, emphasizing dominant and recessive alleles. See how genotype and phenotype relate in homozygous and heterozygous plants, and practice Punnett squares with PKU and Huntington's.

Explore how multiple genes with additive effects and incomplete dominance shape continuous variation in skin colour and height, within genetics and next generation sequencing contexts.

Explore how inheritance patterns arise from two chromosome sets, independent assortment, and chromosomal linkage in allele transmission. Examine X-linked haemophilia, sex linkage, and carrier dynamics in sons and daughters.

Understand how Sanger sequencing uses DNA polymerase and chain-terminating modified nucleotides with fluorescent tags and capillary electrophoresis to read the sequence, limited to about 1000 base pairs per run.

Discover how next generation sequencing works by comparing sanger sequencing with sequencing by synthesis on a flow cell, enabling parallel reads with modified nucleotides and fluorescence to reveal bases.

Learn how to prepare a DNA library for next-generation sequencing by fragmenting DNA, attaching adapters and indices, size-selecting fragments, and enabling multiplexed, accurate reads on a flow cell.

Explore how adapters attach double-stranded fragments to the Illumina flow cell, enabling strand-specific sequencing by synthesis after removing forward strands to produce reads from the reverse strand.

Perform quality checks and discard low quality reads before assembling reads into longer sequences. Map to a reference genome, identify and annotate variants, and visualize them with a genome browser.

Compare whole genome sequencing, whole exome sequencing, and targeted sequencing, and grasp core concepts like depth of coverage, read depth, and breadth of coverage.

Explore how paired end reads from both ends of DNA fragments enhance assembly and variant detection through forward and reverse reads, insert size, inner distance, and anchor reads.

Explore single nucleotide polymorphisms, indels, and larger structural variants, and learn how paired reads detect inversions, insertions, deletions, duplications, copy number variants, and translocations.

Explore how somatic mutations drive cancer by disrupting DNA repair and cell-cycle brakes, and distinguish somatic from germline variants that are inherited.

Understand how somatic variants guide personalized cancer treatment through NGS, distinguishing tumor-specific drivers from germline variants to tailor targeted therapies.

Galaxy, a free web-based platform for next-generation sequencing analysis, lets you run tools like bwa and Picard SortSam through reusable workflows.

Find publicly accessible next-generation sequencing data on the NCBI SRA, apply filters for exome, DNA, and Illumina, and load runs into Galaxy for processing using FASTA or FASTQ downloads.

Explore the fastq data format from a sequencer, including four-line reads, forward and reverse identifiers, interleaved files, and ASCII-encoded quality scores in the Sanger format.

Evaluate sequencing data quality with fastqc by reading quality reports, examining gc content and base quality trends, and learning to trim low-quality ends for illumina reads.

Assess FastQC quality checks to interpret per sequence GC content, duplication levels, and adapter content; learn how duplication biases GC distribution and how de-duplication improves variant calling.