help:

--version

show program's version number and exit

-h, --help

show this help message and exit

subcommands:

Assembly method

align

Assemble pairs by aligning ends.

join

Assemble pairs by concatenating ends.

reference

Assemble pairs by aligning reads against a reference database.

sequential

Assemble pairs by first attempting de novo assembly, then reference guided assembly.

output files:

assemble-pass

successfully assembled reads.

assemble-fail

raw reads failing paired-end assembly.

output annotation fields:

<user defined>

annotation fields specified by the --1f or --2f arguments.