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Assembling Mitogenomes from PacBio HiFi reads using MitoHiFi

This session is part of Biodiversity Genomics Academy 2023

Session Leader(s)

Marcela Uliano-Silva
Senior Bioinformatician, Wellcome Sanger Institute

Description

By the end of this session you will be able to:

  1. Run MitoHiFi using docker
  2. Understand the different steps done by MitoHiFi
  3. Understand intermediate outputs
  4. Cases where the pipeline fails

Prerequisites

  1. Understand the terms genome assembly, reads, contigs, PacBio HiFi
  2. Understand linux command line basics

Please make sure you MEET THE PREREQUISITES and READ THE DESCRIPTION above

You will get the most out of this session if you meet the prerequisites above.

Please also read the description carefully to see if this session is relevant to you.

If you don't meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at sanger.ac.uk to cancel your slot so that someone else on the waitlist might attend.

## Connecting to gitpod for the session

Click here to launch a Gitpod workspace with MitoHiFi

Commands for the session

  1. Let's assemble something pink (from reads, -r)
cd /workspace/lecture_examples/deilephila_porcellus

findMitoReference.py --species "Deilephila porcellus" --outfolder . --min_length 14000

mitohifi.py -r ilDeiPorc1.reads.100.fa -f NC_079697.1.fasta -g NC_079697.1.gb -t 1 -o 5
  1. Let's do a bird (from contigs, -c)
cd /workspace/lecture_examples/cygnus_columbianus

findMitoReference.py --species "Cygnus columbianus" --outfolder . --min_length 14000

mitohifi.py -c bCygCol1.hifiasm.contigs.fa -f NC_007691.1.fasta -g NC_007691.1.gb -o 2 -t 3
  1. Let's do a plant (from contigs, -c)
cd /workspace/lecture_examples/climacium_dendroides

findMitoReference.py --species "Climacium dendroides" --outfolder . --min_length 50000

mitohifi.py -c cbCliDend2.hicanu.contigs.fa -f NC_053886.1.fasta -g NC_053886.1.gb -t 6 -o 1 -a plant