SemiBin2
Starting with version 1.5 (officially SemiBin2 beta), installing the SemiBin
package installs two scripts: SemiBin
and SemiBin2
.
They have the same functionality, but slightly different interfaces. The exact
interface to SemiBin2
should be considered as unstable (while we will strive
to maintain backwards compatibility if you call the SemiBin
script).
Upgrading to SemiBin2
- If you are using the
easy_*
workflows, then they will probably continue to work exactly the same (except that you will get better results faster). - Outputs are now always in a directory called
output_bins
. - By default, bins are in file named as
SemiBin_{label}.fa.gz
(and compressed with gzip as the name indicates).
Points 2
and 3
may require some minor modifications to wrapper scripts.
Longer list of differences between SemiBin2 and SemiBin1
The biggest different is that the default training mode is self-supervised mode.
- Output bins are now always in a directory called
output_bins
(in SemiBin1, it actually depended on which parameters were used) - Output filenames are now anvi'o compatible (effectively, the default value of
--tag-output
isSemiBin
), see discussion at #123. --compression
defaults togz
(instead ofnone
)- ORF finder defaults to the
fast-naive
internal ORF finder --write-pre-reclustering-bins
isFalse
by default- To train in semi-supervised mode, you must use the
train_semi
subcommand (and there is notrain
subcommand, you must be specific:train_semi
ortrain_self
).
A few arguments that were deprecated before are completely removed:
- --recluster
: it did nothing already as reclustering is default
- --mode
: Use --train-from-many
- --training-type
: Use --semi-supervised
to use semi-supervised learning
(although that is also deprecated)