Lecture 11- Bacterial genomics I - Features of bacterial genomes

Question 1

2 approaches to organising short read data

Answer 1

mapping, involving aligning reads to a reference genome
de novo assembly- no reference genome

Question 2

pros and cons of mapping

Answer 2

rapid and easy to visualise, reproducible
requires a reference genome which may not exist, can’t identify genomic events such as translocations and rearrangements

Question 3

pros and cons of de novo assembly

Answer 3

good for novel sequences and identifying large genomic changes
struggles to resolve repetitive regions, time consuming, often misses parts of the genome

Question 4

phred score

Answer 4

quality score for each base, which can be used to help analyse SNPs

Question 5

how does de novo assembly work (2 methods)

Answer 5

‘overlap-layout consensus’- all overlaps between reads are determined, laid out and a consensus sequence is determined
alternatively de brujin graph method- shorter k-mer fragments are generated, and the best links between these reads are determined to assemble a genome

Question 6

example of long-read sequencing technologies

Answer 6

minION (oxford nanopore)

Question 7

important things to note in gene annotation

Answer 7

location, feature type, attributes- e.g. location of protein, enzyme code

Question 8

approximate size of bacterial genomes

Answer 8

2-5mb

Question 9

what is in the ‘core genome’ of bacteria

Answer 9

DNA replication, cell envelope, some metabolic genes

Question 10

example of accessory genes

Answer 10

alternative metabolic pathways, transport systems. antibiotic resistance genes

Question 11

what is a pangenome

Answer 11

set of genes shared by all members of a group