Introduction to Genome assembly

Figure 1

Diagram showing the genome assembly process from fragmented DNA reads to a continuous sequence
Genome Assembly

Figure 2

Chart showing the growth of genome sequences deposited in NCBI over time
Number of genomes in NCBI

Figure 3

Assembly types

Figure 4

Flowchart of the basic steps in genome assembly from sequencing through quality assessment
Steps Overview

Figure 5

Photos of Illumina, PacBio, and Oxford Nanopore sequencing instruments
Sequencing Instruments

Figure 6

Diagram illustrating challenges in genome assembly including repetitive elements, heterozygosity, and structural variants
Challenges in Genome Assembly

Figure 7

Programs used in this workshop

Assembly Strategies

Figure 1

Diagram comparing contig-level, scaffold-level, and chromosome-level genome assemblies
Assembly levels

Figure 2

Workflow diagram for PacBio HiFi assembly using HiFiasm
PacBio Assembly

Figure 3

Workflow diagram for ONT assembly using Flye with Medaka polishing
ONT assembly

Figure 4

Workflow diagram for hybrid assembly combining ONT and PacBio HiFi reads using Flye
Hybrid assembly

Figure 5

BUSCO genes

Figure 6

Example k-mer spectra plot from Merqury showing copy number distribution
kmer spectra

Figure 7

Diagram showing how Bionano OGM and Hi-C data improve genome assembly scaffolding
Bionano and HiC for assembly improvement

Data Quality Control

Figure 1

Flowchart showing data quality control steps: NanoPlot assessment, Filtlong filtering, and post-filtering evaluation
Overview of steps

Figure 2

Diagram showing PacBio circular consensus sequencing generating HiFi reads from multiple passes
PacBio CCS overview

Figure 3

Diagram showing Oxford Nanopore read generation from signal detection through Dorado basecalling
Overview of ONT read generation

Figure 4

KDE scatter plot of PacBio HiFi read length versus average read quality showing a tight cluster of reads between 15-30 kb with quality scores predominantly above Q20
PacBio HiFi read length vs quality

Figure 5

KDE scatter plot of ONT read length versus average read quality showing a broad spread of reads from 1-200 kb with quality scores ranging from Q5 to Q20
ONT read length vs quality

Figure 6

KDE scatter plot of ONT read length versus quality after Filtlong filtering showing reads concentrated between 20-80 kb with the shortest and lowest-quality reads removed
ONT read length vs quality after filtering

PacBio HiFi Assembly using HiFiasm

Figure 1

Overview of the HiFiasm assembly workflow from read overlaps through graph construction to contig generation
HiFiasm assembler

Oxford Nanopore Assembly using Flye

Figure 1

Diagram showing how ultra-long ONT reads enable telomere-to-telomere genome assemblies
ONT for T2T assemblies

Figure 2

Overview of the Flye assembler workflow from disjointig generation through repeat graph construction to polished contigs
Flye assembly overview

Hybrid Long Read Assembly (optional)

Scaffolding using Optical Genome Mapping

Figure 1

Diagram showing the Bionano optical genome mapping process from DNA labeling to genome-wide maps
Overview of Bionano OGM

Figure 2

Workflow diagram of Bionano Solve hybrid scaffolding pipeline showing in silico map generation, conflict resolution, and scaffold assembly
Scaffolding using Bionano

Assembly Assessment

Figure 1

Merqury copy number spectrum plot for the hifiasm Bionano-scaffolded assembly showing a sharp unimodal peak at approximately 30x indicating a homozygous genome with high completeness
Merqury copy number spectrum

Figure 2

Merqury assembly spectrum plot comparing k-mers found in the assembly versus read-only k-mers showing most k-mers are shared between reads and assembly
Merqury assembly spectrum

Figure 3

Screenshot of the Bandage application showing an assembly graph visualization with connected contigs
Bandage interface