CollapseSeq¶
Removes duplicate sequences from FASTA/FASTQ files
usage: CollapseSeq [--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] [-n MAX_MISSING]
[--uf UNIQ_FIELDS [UNIQ_FIELDS ...]]
[--cf COPY_FIELDS [COPY_FIELDS ...]]
[--act {min,max,sum,set} [{min,max,sum,set} ...]] [--inner]
[--keepmiss] [--maxf MAX_FIELD | --minf MIN_FIELD]
-
--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.
-
-n
<max_missing>
¶ Maximum number of missing nucleotides to consider for collapsing sequences. A sequence will be considered undetermined if it contains too many missing nucleotides.
-
--uf
<uniq_fields>
¶ Specifies a set of annotation fields that must match for sequences to be considered duplicates.
-
--cf
<copy_fields>
¶ Specifies a set of annotation fields to copy into the unique sequence output.
-
--act
{min,max,sum,set}
¶ 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” collapses annotations into a comma delimited list of unique values.
-
--inner
¶
If specified, exclude consecutive missing characters at either end of the sequence.
-
--keepmiss
¶
If specified, sequences with more missing characters than the threshold set by the -n parameter will be written to the unique sequence output file with a DUPCOUNT=1 annotation. If not specified, such sequences will be written to a separate file.
-
--maxf
<max_field>
¶ Specify the field whose maximum value determines the retained sequence; mutually exclusive with –minf.
-
--minf
<min_field>
¶ Specify the field whose minimum value determines the retained sequence; mutually exclusive with –minf.
- output files:
- collapse-unique
- unique sequences. Contains one representative from each set of duplicate sequences. The retained representative is determined by user defined criteria.
- collapse-duplicate
- raw reads which are duplicates of the sequences retained in the collapse-unique file.
- collapse-undetermined
- raw reads which were excluded from consideration due to having too many N characters in the sequence.
- output annotation fields:
- DUPCOUNT
- total number of sequences within the set of duplicates for each retained unique sequence. Meaning, the copy number of each unique sequence within the data file.
- <user defined>
- annotation fields specified by the –cf parameter.