#BGA23/sessions#MitoHiFi#Assembly#Mitochondrion#PacBio#Pipeline#Workshop
This session may now be out of date so beware!!!
This session is part of BGA23
Session Leader(s)
Marcela Uliano-Silva
Senior Bioinformatician, Wellcome Sanger Institute
Description
GitHub:: https://github.com/BGAcademy23/MitoHiFi
By the end of this session you will be able to:
- Run MitoHiFi using docker
- Understand the different steps done by MitoHiFi
- Understand intermediate outputs
- Cases where the pipeline fails
Prerequisites
- Understand the terms genome assembly, reads, contigs, PacBio HiFi
- Understand linux command line basics
!!! warning "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
- 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
- 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
- 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