optional arguments:¶

-h, --help

show this help message and exit

Main options:¶

-i INPUT, --input INPUT

FASTA/FASTQ of input reads or a directory which willbe recursively searched for FASTQ files (required)

-o OUTPUT, --output OUTPUT

Filename for FASTA or FASTQ of trimmed reads (if notset, trimmed reads will be printed to stdout)

--format {auto,fasta,fastq,fasta.gz,fastq.gz}

Output format for the reads - if auto, the formatwill be chosen based on the output filename or theinput 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 readsare saved to a file and stderr if reads are printedto 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

Barcode binning settings:¶

Control the binning of reads based on barcodes (i.e. barcodedemultiplexing)

-b BARCODE_DIR, --barcode_dir BARCODE_DIR

Reads will be binned based on their barcode andsaved to separate files in this directory(incompatible with --output)

--barcode_threshold BARCODE_THRESHOLD

A read must have at least this percent identity to abarcode to be binned (default: 75.0)

--barcode_diff BARCODE_DIFF

If the difference between a read's best barcodeidentity and its second-best barcode identity isless than this value, it will not be put in abarcode bin (to exclude cases which are too close tocall) (default: 5.0)

--require_two_barcodes

Reads will only be put in barcode bins if they havea strong match for the barcode on both their startand end (default: a read can be binned with a matchat its start or end)

--untrimmed

Bin reads but do not trim them (appropriate if readsare to be used with Nanopolish) (default: trim thereads)

--discard_unassigned

Discard unassigned reads (instead of creating a"none" bin) (default: False)

Adapter search settings:¶

Control how the program determines which adapter sets are present

--adapter_threshold ADAPTER_THRESHOLD

An adapter set has to have at least this percentidentity 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 possibleadapters 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)

End adapter settings:¶

Control the trimming of adapters from read ends

--end_size END_SIZE

The number of base pairs at each end of the readwhich 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 toadapters found at the ends of reads (default: 2)

--end_threshold END_THRESHOLD

Adapters at the ends of reads must have at leastthis percent identity to be removed (0 to 100)(default: 75.0)

Middle adapter settings:¶

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 inthe 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 readsinto barcode bins)

--middle_threshold MIDDLE_THRESHOLD

Adapters in the middle of reads must have at leastthis 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 tomiddle 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 tomiddle adapters on their "bad" side (default: 100)

--min_split_read_size MIN_SPLIT_READ_SIZE

Post-split read pieces smaller than this many basepairs will not be outputted (default: 1000)