BuildConsensus.py

NAME

BuildConsensus.py - Builds a consensus sequence for each set of input sequences

DESCRIPTION

usage: BuildConsensus.py [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]

[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]

[--outname OUT_NAME] [--log LOG_FILE] [--failed] [--fasta] [--delim DELIMITER DELIMITER DELIMITER] [--nproc NPROC] [-n MIN_COUNT] [--bf BARCODE_FIELD] [-q MIN_QUAL] [--freq MIN_FREQ] [--maxgap MAX_GAP] [--pf PRIMER_FIELD] [--prcons PRIMER_FREQ] [--cf COPY_FIELDS [COPY_FIELDS ...]] [--act {min,max,sum,set,majority} [{min,max,sum,set,majority} ...]] [--dep] [--maxdiv MAX_DIVERSITY | --maxerror MAX_ERROR]

Builds a consensus sequence for each set of input sequences

help:

--version

show program's version number and exit

-h, --help

show this help message and exit

standard arguments:

-s SEQ_FILES [SEQ_FILES ...]

A list of FASTA/FASTQ files containing sequences to process. (default: None)

-o OUT_FILES [OUT_FILES ...]

Explicit output file name(s). Note, this argument cannot be used with the --failed, --outdir, or --outname arguments. If unspecified, then the output filename will be based on the input filename(s). (default: None)

--outdir OUT_DIR

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified. (default: None)

--outname OUT_NAME

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files. (default: None)

--log LOG_FILE

Specify to write verbose logging to a file. May not be specified with multiple input files. (default: None)

--failed

If specified create files containing records that fail processing. (default: False)

--fasta

Specify to force output as FASTA rather than FASTQ. (default: None)

--delim DELIMITER DELIMITER DELIMITER

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively. (default: ('|', '=', ','))

--nproc NPROC

The number of simultaneous computational processes to execute (CPU cores to utilized). (default: 4)

consensus generation arguments:

-n MIN_COUNT

The minimum number of sequences needed to define a valid consensus. (default: 1)

--bf BARCODE_FIELD

Position of description barcode field to group sequences by. (default: BARCODE)

-q MIN_QUAL

Consensus quality score cut-off under which an ambiguous character is assigned; does not apply when quality scores are unavailable. (default: 0)

--freq MIN_FREQ

Fraction of character occurrences under which an ambiguous character is assigned. (default: 0.6)

--maxgap MAX_GAP

If specified, this defines a cut-off for the frequency of allowed gap values for each position. Positions exceeding the threshold are deleted from the consensus. If not defined, positions are always retained. (default: None)

--pf PRIMER_FIELD

Specifies the field name of the primer annotations (default: None)

--prcons PRIMER_FREQ

Specify to define a minimum primer frequency required to assign a consensus primer, and filter out sequences with minority primers from the consensus building step. (default: None)

--cf COPY_FIELDS [COPY_FIELDS ...]

Specifies a set of additional annotation fields to copy into the consensus sequence annotations. (default: None)

--act {min,max,sum,set,majority} [{min,max,sum,set,majority} ...]

List of actions to take for each copy field which defines how each annotation will be combined into a single value. The actions "min", "max", "sum" perform the corresponding mathematical operation on numeric annotations. The action "set" combines annotations into a comma delimited list of unique values and adds an annotation named <FIELD>_COUNT specifying the count of each item in the set. The action "majority" assigns the most frequent annotation to the consensus annotation and adds an annotation named <FIELD>_FREQ specifying the frequency of the majority value. (default: None)

--dep

Specify to calculate consensus quality with a nonindependence assumption (default: False)

--maxdiv MAX_DIVERSITY

Specify to calculate the nucleotide diversity of each read group (average pairwise error rate) and remove groups exceeding the given diversity threshold. Diversity is calculate for all positions within the read group, ignoring any character filtering imposed by the -q, --freq and --maxgap arguments. Mutually exclusive with --maxerror. (default: None)

--maxerror MAX_ERROR

Specify to calculate the error rate of each read group (rate of mismatches from consensus) and remove groups exceeding the given error threshold. The error rate is calculated against the final consensus sequence, which may include masked positions due to the -q and --freq arguments and may have deleted positions due to the --maxgap argument. Mutually exclusive with --maxdiv. (default: None)

output files:

consensus-pass

consensus reads.

consensus-fail

raw reads failing consensus filtering criteria.

output annotation fields:

PRIMER

a comma delimited list of unique primer annotations found within the barcode read group.

PRCOUNT

a comma delimited list of the corresponding counts of unique primer annotations.

PRCONS

the majority primer within the barcode read group.

PRFREQ

the frequency of the majority primer.

CONSCOUNT

the count of reads within the barcode read group which contributed to the consensus sequence. This is the total size of the read group, minus sequence excluded due to user defined filtering criteria.

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.