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 ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--delim DELIMITER DELIMITER DELIMITER]
[--nproc NPROC] [--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.
-
-o
<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).
-
--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.
-
--log
<log_file>
¶ Specify to write verbose logging to a file. May not be specified with multiple input files.
-
--failed
¶
If specified create files containing records that fail processing.
-
--fasta
¶
Specify to force output as FASTA rather than FASTQ.
-
--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).
-
--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 ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--delim DELIMITER DELIMITER DELIMITER]
[--nproc NPROC] [-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.
-
-o
<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).
-
--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.
-
--log
<log_file>
¶ Specify to write verbose logging to a file. May not be specified with multiple input files.
-
--failed
¶
If specified create files containing records that fail processing.
-
--fasta
¶
Specify to force output as FASTA rather than FASTQ.
-
--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).
-
-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] [--outdir OUT_DIR]
[--outname OUT_NAME] [--failed]
[--delim DELIMITER DELIMITER DELIMITER] -p PRIMER_FILE
[-o OUT_FILE] [--reverse] [--exec ALIGNER_EXEC]
-
--version
¶
show program’s version number and exit
-
-h
,
--help
¶
show this help message and exit
-
--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.
-
--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.
-
-p
<primer_file>
¶ A FASTA file containing primer sequences.
-
-o
<out_file>
¶ Explicit output file name. 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).
-
--reverse
¶
If specified create a 3’ offset table instead
-
--exec
<aligner_exec>
¶ The name or location of the muscle executable.