AlignSets

Multiple aligns input sequences by group

usage: AlignSets [--version] [-h]  ...
--version

show program’s version number and exit

-h, --help

show this help message and exit

output files:
align-pass
multiple aligned reads.
align-fail
raw reads failing multiple alignment.
offsets-forward
5’ offset table for input into offset subcommand.
offsets-reverse
3’ offset table for input into offset subcommand.
output annotation fields:
None

AlignSets muscle

Align sequence sets using muscle.

usage: AlignSets muscle [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                            [--fasta] [--failed] [--log LOG_FILE]
                            [--delim DELIMITER DELIMITER DELIMITER]
                            [--nproc NPROC] [--outdir OUT_DIR]
                            [--outname OUT_NAME] [--bf BARCODE_FIELD] [--div]
                            [--exec ALIGNER_EXEC]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-s <seq_files>

A list of FASTA/FASTQ files containing sequences to process.

--fasta

Specify to force output as FASTA rather than FASTQ.

--failed

If specified create files containing records that fail processing.

--log <log_file>

Specify to write verbose logging to a file. May not be specified with multiple input files.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--nproc <nproc>

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

--outdir <out_dir>

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.

--outname <out_name>

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.

--bf <barcode_field>

The annotation field containing barcode labels for sequence grouping.

--div

Specify to calculate nucleotide diversity of each set (average pairwise error rate).

--exec <aligner_exec>

The name or location of the muscle executable.

AlignSets offset

Align sequence sets using predefined 5’ offset.

usage: AlignSets offset [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                            [--fasta] [--failed] [--log LOG_FILE]
                            [--delim DELIMITER DELIMITER DELIMITER]
                            [--nproc NPROC] [--outdir OUT_DIR]
                            [--outname OUT_NAME] [-d OFFSET_TABLE]
                            [--bf BARCODE_FIELD] [--pf PRIMER_FIELD]
                            [--mode {pad,cut}] [--div]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-s <seq_files>

A list of FASTA/FASTQ files containing sequences to process.

--fasta

Specify to force output as FASTA rather than FASTQ.

--failed

If specified create files containing records that fail processing.

--log <log_file>

Specify to write verbose logging to a file. May not be specified with multiple input files.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--nproc <nproc>

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

--outdir <out_dir>

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.

--outname <out_name>

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.

-d <offset_table>

The tab delimited file of offset tags and values.

--bf <barcode_field>

The annotation field containing barcode labels for sequence grouping.

--pf <primer_field>

The primer field to use for offset assignment.

--mode {pad,cut}

Specifies whether or align sequence by padding with gaps or by cutting the 5’ sequence to a common start position.

--div

Specify to calculate nucleotide diversity of each set (average pairwise error rate).

AlignSets table

Create a 5’ offset table by primer multiple alignment.

usage: AlignSets table [--version] [-h] [--failed]
                           [--delim DELIMITER DELIMITER DELIMITER]
                           [--outdir OUT_DIR] [--outname OUT_NAME] -p PRIMER_FILE
                           [--reverse] [--exec ALIGNER_EXEC]
--version

show program’s version number and exit

-h, --help

show this help message and exit

--failed

If specified create files containing records that fail processing.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--outdir <out_dir>

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.

--outname <out_name>

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.

-p <primer_file>

A FASTA or REGEX file containing primer sequences

--reverse

If specified create a 3’ offset table instead

--exec <aligner_exec>

The name or location of the muscle executable