COMPUTATIONAL GENOMICS

Genome Assembly

De Novo vs Reference Assembly

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Consistency of De Novo Assembly

Choice of Assembler

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Assembly Quality Comparison

SkesaSpadesUnicyclerMaSuRCA

Genome Assembly Pipeline

Gene Prediction &

Functional Annotation

Objectives

Merge

Merge

Merge

Gene Prediction Pipeline

Gene Prediction Results

Coding Regions Non coding Regions

Functional Annotation Pipeline

gff

Signal Peptides: SignalP-4.1

Lipoproteins and TM Proteins: LipoP

Genome

No. of Hits

Avg: 967 genes per genome

Genome

No. of Hits

Operons: DOOR2

Avg: 280 genes per genome

eggNOG-mapper

CRISPR: PILER-CRTotal 84 hits among 50 genomes

Prophage: PHASTER (PHAge Search Tool Enhanced Release)

Antibiotic Resistance: RGI

Avg: 43 genes per genome

Fosfomycin inactivating enzyme (FosA5 or FosA6) present in all the genomes

Virulence Factors: VFDB + Victor

Genome

No. of Hits

SRR4017925 Avg: 36 genes per genome

Comparative Genomics

Comparative Genomics Pipeline

Predict

ST258

Similarity Analysis

Presence or Absence of Genes

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Intergenic Regions

Multilocus Sequence Typing

HeteroresistantResistantSusceptible

kSNP3.0

Conclusion?

Predictive Web Server Demo

Extra Slides

Gene Prediction Results - BLAST+ Results%

Bla

st H

its

SRR5666568

SRR5666568

Coding Regions Non-Coding Regions