domainator deduplicate_genbank
Reduce redundancy by clustering sequences (cd-hit, usearch, diamond, or exact hashes).
Remove redundant sequences from a genbank file
Runs a clustering algorithm, such as cdhit, usearch, or diamond on sequences from a genbank (or fasta) file to reduce redundancy.
The "hash" algorithm is a faster way to deduplicate exact duplicates, by hashing the sequences and eliminating hash duplicates.
Give at least one of these outputs: --genbank_out, --fasta_out. - as an input or output means standard input or output, where the option says it is allowed.
| Option | Value | Default | Description |
|---|---|---|---|
-v, --verbose |
show debug output, and a traceback for errors. | ||
-q, --quiet |
show errors only: no progress messages or warnings. | ||
-i, --input |
FILE ... | required | GenBank or FASTA files. |
-o, --genbank_out |
FILE | Write the records to this GenBank file. Use - for standard output. | |
--fasta_out |
FILE | Write the records to this FASTA file. Use - for standard output. | |
--log_out |
FILE | Write the log to this file. If not supplied, writes it to stderr. | |
--alphabet |
{nucleotide,protein} | protein | Whether the sequences in FASTA inputs are protein or nucleotide. GenBank records declare their own molecule type. |
--algorithm |
{cd-hit,usearch,hash,diamond} | cd-hit | Which clustering algorithm to use. |
--cdhit_path |
PROGRAM | path to the cd-hit executable, if it is not on the PATH. | |
--cdhit_est_path |
PROGRAM | path to the cd-hit-est executable, if it is not on the PATH. | |
--usearch_path |
PROGRAM | path to the usearch executable, if it is not on the PATH. | |
--diamond_path |
PROGRAM | path to the diamond executable, if it is not on the PATH. | |
--identity, --id |
NUMBER | required | Identity threshold (between 0 and 1), passed to cd-hit as the -c parameter, to usearch as the -id parameter, or to diamond as --approx-id after converting to percent. |
--prefix_count |
In the output genbank file, will prepend X- to the names of contigs, where X is the number of contigs from the original file collapsed into this centroid. | ||
--suffix_count |
In the output genbank file, will append -X to the names of contigs, where X is the number of contigs from the original file collapsed into this centroid. | ||
--cpu |
INTEGER | 0 | The number of threads to use for deduplication. 0: one per physical core. |
--cdhit_args |
STRING | extra options for cd-hit or cd-hit-est, as one quoted string split like a shell command line. Use the = form: --cdhit_args="-s 0.9". Options that domainator sets itself are refused. | |
--usearch_args |
STRING | extra options for usearch, as one quoted string split like a shell command line. Use the = form: --usearch_args="-s 0.9". Options that domainator sets itself are refused. | |
--diamond_args |
STRING | extra options for diamond cluster, as one quoted string split like a shell command line. Use the = form: --diamond_args="-s 0.9". Options that domainator sets itself are refused. | |
--both_strands |
When set for nucleotide inputs, consider both strands for clustering/hash deduplication. | ||
--cluster_tsv_out |
FILE | If supplied, then write a tab separated table with columns: representative, contigs. | |
--cluster_sep |
STRING | ; | Separator to separate individual contig names in the second column of the cluster table. |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.