AlignSets

Multiple aligns input sequences by group

usage: AlignSets [-h] [–version] ...

-h, --help

show this help message and exit

--version

show program’s version number 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 [-h] [–version] ...

-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 <muscle_exec>

The location of the MUSCLE executable

AlignSets offset

Align sequence sets using predefined 5’ offset

usage: AlignSets [-h] [–version] ...

-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)

-d <offset_table>

The tab delimited file of offset tags and values

--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

AlignSets table

Create a 5’ offset table by primer multiple alignment

usage: AlignSets [-h] [–version] ...

-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 <muscle_exec>

The location of the MUSCLE executable