Open HadrienG opened 7 years ago
The project aims at building a modular pipeline for de-novo bacterial assembly using nanopore reads.
Preliminary plan:
If time permits it:
(the workflow is open to software suggestions and improvements)! 😄
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.
fasta
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.
The project will be led by Hadrien Gourlé
I will join in on this
Kind regards
Me too!
I will join
Kind regards,
Mauro
Dev happening at https://github.com/HadrienG/nanoflow 🎉
Project
The project aims at building a modular pipeline for de-novo bacterial assembly using nanopore reads.
Preliminary plan:
If time permits it:
(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