Circularizing plasmid assemblies

[danejo3]

In the original code of runMA, assembling circularized plasmids was implemented and has yet to migrate over to YEAT.

Before this feature can be implemented, a few things need to be done.

1. Check and see if the circularized plasmids code is working.
2. Understand what it does.
3. Maybe look into various other assemblers that focus primarily on bacterial genome circularization?

[danejo3]

runMA use(d)/(s) Unicycler. Here are some notes recently made by the author of the tool.

[danejo3]

Found a list of assemblers recommended by the Unicycler author depending on the read length and situations--focusing on bacteria genomes.

Short reads

• SKESA - for very accurate contigs with minimal misassemblies
• SPAdes - for very reproducible assembly
• Unicycler - for most short-read bacterial genome assemblies (uses spades and add it's own touches for circularization)

Long reads

• Raven - Computational performance is important--speed
• Flye - Assembly accuracy is important, slow
• Trycycler - even further accuracy, slower

[danejo3]

Long reads, when assembled, needs polishing.

• arrow
• quiver