optionalarguments:-h, --help
show this help message and exit
Mainoptions:-i INPUT, --input INPUT
FASTA/FASTQ of input reads or a directory which will be recursively searched for FASTQ files
(required)
-o OUTPUT, --output OUTPUT
Filename for FASTA or FASTQ of trimmed reads (if not set, trimmed reads will be printed to stdout)
--format {auto,fasta,fastq,fasta.gz,fastq.gz}
Output format for the reads - if auto, the format will be chosen based on the output filename or
the input read format (default: auto)
-v VERBOSITY, --verbosity VERBOSITY
Level of progress information: 0 = none, 1 = some, 2 = lots, 3 = full - output will go to stdout
if reads are saved to a file and stderr if reads are printed to stdout (default: 1)
-t THREADS, --threads THREADS
Number of threads to use for adapter alignment (default: 4)
--version
show program's version number and exit
Barcodebinningsettings:
Control the binning of reads based on barcodes (i.e. barcode demultiplexing)
-b BARCODE_DIR, --barcode_dir BARCODE_DIR
Reads will be binned based on their barcode and saved to separate files in this directory
(incompatible with --output)
--barcode_threshold BARCODE_THRESHOLD
A read must have at least this percent identity to a barcode to be binned (default: 75.0)
--barcode_diff BARCODE_DIFF
If the difference between a read's best barcode identity and its second-best barcode identity is
less than this value, it will not be put in a barcode bin (to exclude cases which are too close to
call) (default: 5.0)
--require_two_barcodes
Reads will only be put in barcode bins if they have a strong match for the barcode on both their
start and end (default: a read can be binned with a match at its start or end)
--untrimmed
Bin reads but do not trim them (appropriate if reads are to be used with Nanopolish) (default:
trim the reads)
--discard_unassigned
Discard unassigned reads (instead of creating a "none" bin) (default: False)
Adaptersearchsettings:
Control how the program determines which adapter sets are present
--adapter_threshold ADAPTER_THRESHOLD
An adapter set has to have at least this percent identity to be labelled as present and trimmed
off (0 to 100) (default: 90.0)
--check_reads CHECK_READS
This many reads will be aligned to all possible adapters to determine which adapter sets are
present (default: 10000)
--scoring_scheme SCORING_SCHEME
Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend (default:
3,-6,-5,-2)
Endadaptersettings:
Control the trimming of adapters from read ends
--end_size END_SIZE
The number of base pairs at each end of the read which will be searched for adapter sequences
(default: 150)
--min_trim_size MIN_TRIM_SIZE
Adapter alignments smaller than this will be ignored (default: 4)
--extra_end_trim EXTRA_END_TRIM
This many additional bases will be removed next to adapters found at the ends of reads (default:
2)
--end_threshold END_THRESHOLD
Adapters at the ends of reads must have at least this percent identity to be removed (0 to 100)
(default: 75.0)
Middleadaptersettings:
Control the splitting of read from middle adapters
--no_split
Skip splitting reads based on middle adapters (default: split reads when an adapter is found in
the middle)
--discard_middle
Reads with middle adapters will be discarded (default: reads with middle adapters are split) (this
option is on by default when outputting reads into barcode bins)
--middle_threshold MIDDLE_THRESHOLD
Adapters in the middle of reads must have at least this percent identity to be found (0 to 100)
(default: 85.0)
--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE
This many additional bases will be removed next to middle adapters on their "good" side (default:
10)
--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE
This many additional bases will be removed next to middle adapters on their "bad" side (default:
100)
--min_split_read_size MIN_SPLIT_READ_SIZE
Post-split read pieces smaller than this many base pairs will not be outputted (default: 1000)
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