Project 10: De novo assembly of nanopore reads

[HadrienG]

Project

The project aims at building a modular pipeline for de-novo bacterial assembly using nanopore reads.

Preliminary plan:

• adapter trimming using porechop
• assembly using:
  • canu
  • miniasm
• polishing using:
  • racon
  • nanopolish
• circularisation using circlator

If time permits it:

• annotation using prokka
• format conversion using gff3toembl

(the workflow is open to software suggestions and improvements)! 😄

Data:

We'll use a subset of E. coli data from a R9 run from here

We'll work directly with the fasta files (1.5G) to avoid to lose time on the basecalling.

Computing resources:

About 20GB of RAM is necessary for miniasm. 8 cores would be great but we could manage with 4. I think a t2.2xlarge or an r4.xlarge would suffice.

Project Lead:

The project will be led by Hadrien Gourlé

[Ackia]

I will join in on this

Kind regards

[jhayer]

Me too!

[mauropetrillo]

I will join

Kind regards,

Mauro

[HadrienG]

Dev happening at https://github.com/HadrienG/nanoflow 🎉