Tools

Bin Chicken coassemble

coassemble is the primary command used to cluster samples using unbinned single-copy marker genes and assemble/recover as suggested.

Bin Chicken update

update allows you to apply further processing to a previous Bin Chicken run (e.g. actually running assembly/recovery, generating unmapped reads files, and/or downloading SRA reads).

Bin Chicken iterate

iterate enables an iterative workflow, where new coassemblies are suggested, searching for novelty based on old and newly recovered bins.

Bin Chicken evaluate

evaluate is used to evaluate the targeting success of a Bin Chicken run.

Bin Chicken build

build generates all dependency conda environments and sets environment variables. Ideal for first-time use.