FilterSeq¶
Filters sequences in FASTA/FASTQ files
usage: FilterSeq [--version] [-h] ...
-
--version
¶
show program’s version number and exit
-
-h
,
--help
¶
show this help message and exit
- output files:
- <command>-pass
- reads passing filtering operation and modified accordingly, where <command> is the name of the filtering operation that was run.
- <command>-fail
- raw reads failing filtering criteria, where <command> is the name of the filtering operation.
- output annotation fields:
- None
FilterSeq length¶
Filters reads by length.
usage: FilterSeq length [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--nproc NPROC] [-n MIN_LENGTH] [--inner]
-
--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.
-
--nproc
<nproc>
¶ The number of simultaneous computational processes to execute (CPU cores to utilized).
-
-n
<min_length>
¶ Minimum sequence length to retain.
-
--inner
¶
If specified exclude consecutive missing characters at either end of the sequence.
FilterSeq maskqual¶
Masks low quality positions.
usage: FilterSeq maskqual [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--nproc NPROC] [-q MIN_QUAL]
-
--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.
-
--nproc
<nproc>
¶ The number of simultaneous computational processes to execute (CPU cores to utilized).
-
-q
<min_qual>
¶ Quality score threshold.
FilterSeq missing¶
Filters reads by N or gap character count.
usage: FilterSeq missing [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--nproc NPROC] [-n MAX_MISSING] [--inner]
-
--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.
-
--nproc
<nproc>
¶ The number of simultaneous computational processes to execute (CPU cores to utilized).
-
-n
<max_missing>
¶ Threshold for fraction of gap or N nucleotides.
-
--inner
¶
If specified exclude consecutive missing characters at either end of the sequence.
FilterSeq quality¶
Filters reads by quality score.
usage: FilterSeq quality [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--nproc NPROC] [-q MIN_QUAL] [--inner]
-
--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.
-
--nproc
<nproc>
¶ The number of simultaneous computational processes to execute (CPU cores to utilized).
-
-q
<min_qual>
¶ Quality score threshold.
-
--inner
¶
If specified exclude consecutive missing characters at either end of the sequence.
FilterSeq repeats¶
Filters reads by consecutive nucleotide repeats.
usage: FilterSeq repeats [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--nproc NPROC] [-n MAX_REPEAT] [--missing]
[--inner]
-
--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.
-
--nproc
<nproc>
¶ The number of simultaneous computational processes to execute (CPU cores to utilized).
-
-n
<max_repeat>
¶ Threshold for fraction of repeating nucleotides.
-
--missing
¶
If specified count consecutive gap and N characters ‘ in addition to {A,C,G,T}.
-
--inner
¶
If specified exclude consecutive missing characters at either end of the sequence.
FilterSeq trimqual¶
Trims sequences by quality score decay.
usage: FilterSeq trimqual [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--nproc NPROC] [-q MIN_QUAL]
[--win WINDOW] [--reverse]
-
--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.
-
--nproc
<nproc>
¶ The number of simultaneous computational processes to execute (CPU cores to utilized).
-
-q
<min_qual>
¶ Quality score threshold.
-
--win
<window>
¶ Nucleotide window size for moving average calculation.
-
--reverse
¶
Specify to trim the head of the sequence rather than the tail.