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.

Read the Docs v: 0.5.13

Versions: latest; stable; 0.5.13; 0.5.12; 0.5.11; version-0.5.10

Downloads

On Read the Docs: Project Home; Builds

Free document hosting provided by Read the Docs.