Best pipeline / resources / tools for whole genome assembly in a haploid organism

Question

[Mark]

I have to do a lot of nanopore 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

[Dave Carlson]

For microbial genome assembly, I've had a good experience using the Bactopia pipeline, which incidentally just had a major update.

That said, I'm not certain if reference-guided assembly is supported (my suspicion is that it is not).

Answer 2

[GenoMax]

Options mentioned here are still valid. shasta is the latest if you have enough RAM: Assembler for only nanopore data

This is a pretty comprehensive list of software: https://long-read-tools.org/tools.html?sort=Name&cat=&tec=