COMPUTATIONAL GENOMICS
Genome Assembly
De Novo vs Reference Assembly
●
●○○
●○
Consistency of De Novo Assembly
Choice of Assembler
●○
○
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
⇒
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
Top Related