ASM_Bonatelli_Part4

Part 4 of a 4 part series at World Microbe Forum June 2021
Hands-On Workshop Assembling and Annotating Bacterial Genomes Using PacBio Long Reads
https://www.abstractsonline.com/pp8/#!/9286/session/1039
https://ucdavis-bioinformatics-training.github.io/2021-ASM-genome-assembly/

Sequencing technology has changed a lot in the last decades, impacting the amount and the type of data generated. Current long read sequencers, such as PacBio, can generate sequences with tens to hundreds of thousands of base pairs. One of the main advantages of using long reads to assemble a genome is the better resolution in repetitive regions, often leading to assemblies with fewer contigs or even complete chromosomes. However, generating long reads from single-molecules can lead to high-noise sequences, so the proper choice in preprocessing and assembler is imperative.Bacterial genomes are commonly around a few megabase pairs of size and the use of long reads to assemble it can often lead to near-complete or complete chromosomes and plasmids. With long reads sequences, preprocessing and the proper assembly and polishing methodologies, one can have high-quality bacterial genome in only a few steps!This workshop aims to provide to the participants the basic knowledge from beginning to end to assemble near-complete or complete high-quality bacterial genomes from PacBio long reads. Identification of possible plasmid sequences, annotating the genome, and concludes with files ready to submit to NCBI. The hands-on portion of the workshop will involve command-line interaction, so prior command-line experience is important, although a quick introduction in command-line will be provided prior workshop.In summary, the Hands-on Workshop assembling and annotating Bacterial genomes using PacBio long reads will cover:- basic stats of PacBio long reads;- strategies to assemble;- polish and quality check;- tools to annotate the high-quality genome.