BGA Pipeline

(Bacterial Genome Analysis Piplene)

Anwesh Maile

Sessions

DNA Sequencing

Linux Terminal

Raw Reads QC

Mapping & Assembly

Contig Management

Assembly QC

Annotation

Analyses

Topics covered...

  1. Introduction to DNA Sequencing technologies

    Sequencing Generations & Sequencing Platforms

  2. Introduction to Linux Terminal

    Basic commands

  3. DNA Sequence File Formats and Terminology

    FASTQ, Phred Score, N50, Insert Size, etc...

  4. Raw Reads - Quality Control

    Tools: FASTQC, Trimmomatic, and BBDuk

  5. Filtered Reads - Mapping and Assembly

    Reference Mapping: BWA, samtools | de novo Assembly: SPAdes

  6. Sorting the Contigs

    Tools: MeDuSa, Mauve

  7. Minimizing the Gaps and Polishing the Assembly

    Tools: GapCloser, Pilon, Bowtie2, and samtools

  8. Assembly - Quality Control

    Tools: BUSCO, CheckM

  9. Genome Annotation

    Tools: Prokka and RAST server

  10. Visualization and Analyses

    Tools: Circos (Visualization), Roary (Pangenome Analysis), MAFFT and RaxML (Phylogeny), TYGS (Type Strain Detection), antiSMASH (Secondary Metabolite Detection)