commands.rst

Available Commands

Below is a list of the available Chewbacca commands.

preclean

Error Correction

Note: This functionality is still untested and can over correct legitimate variation .. autoclass:: preclean.Preclean_Command.Preclean_Command :members:

Assembling Sequences

assemble.Assemble_Command.Assemble_Command

Demultiplexing by Barcode

demux.Demux_Barcode_Command.Demux_Barcode_Command

Demultiplexing by Name

demux.Demux_Name_Command.Demux_Name_Command

Sequence Renaming

rename.Rename_Command.Rename_Command

Adapter Removal

clean.Clean_Adapters_Command.Clean_Adapters_Command

Quality Cleaning

clean.Clean_Quality_Command.Clean_Quality_Command

File Conversion

util.Convert_Fastq_Fasta_Command.Convert_Fastq_Fasta_Command

Dereplication

dereplicate.Dereplicate_Command.Dereplicate_Command

File Splitting

util.Partition_Command.Partition_Command

File Merging

util.Merge_Command.Merge_Command

File Cleaning

util.Ungap_Command.Ungap_Command

Deep Cleaning

clean.Clean_Deep_Command.Clean_Deep_Command

Deep Cleaning Repair ------------------.. autoclass:: clean.Clean_Deep_Repair_Command.Clean_Deep_Repair_Command :members:

Sequence Clustering

cluster.Cluster_Command.Cluster_Command

OTU Table Construction

otu.Build_OTU_Table_Command.Build_OTU_Table_Command

OTU Identification

otu.Query_OTU_DB_Command.Query_OTU_DB_Command

otu.Query_OTU_Fasta_Command.Query_OTU_Fasta_Command

OTU Annotation

otu.Annotate_OTU_Table_Command.Annotate_OTU_Table_Command