Best pipeline / resources / tools for whole genome assembly

Question

[Mark]

I have to do a lot of sequencing of novel microbes and assemble their genomes. We have a nanopore sequencer and I’ve done a lot of library prep and some bioinformatics work but it’s been mainly for read mapping and not genome assembly. We have microbrial samples that have old reference genomes already and microbes that we don’t have genomes. I’m wondering if anyone could provide me with a list of tools or resources to go about performing whole genome assembly both de novo and using a reference. Thank you!

Answer 1

[Asaf]

Flye should be the state of the art for long reads mapping. Take a look at nf-core/bacass for a comprehensive pipeline (using other tools though).

Answer 2

[Mark]

Worth checking out ONT pipelines here: https://labs.epi2me.io/wfindex/

Of interest is this pipeline in particular: https://github.com/epi2me-labs/wf-bacterial-genomes

If you are new to using the CLI, checkout galaxy which has integrated a lot of the long read tools: https://nanopore.usegalaxy.eu/

Lots of resources on https://training.galaxyproject.org/