Porechop

usage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY] [-t THREADS]
                [-b BARCODE_DIR] [--barcode_threshold BARCODE_THRESHOLD] [--barcode_diff BARCODE_DIFF]
                [--require_two_barcodes] [--untrimmed] [--discard_unassigned] [--adapter_threshold ADAPTER_THRESHOLD]
                [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] [--end_size END_SIZE]
                [--min_trim_size MIN_TRIM_SIZE] [--extra_end_trim EXTRA_END_TRIM] [--end_threshold END_THRESHOLD]
                [--no_split] [--discard_middle] [--middle_threshold MIDDLE_THRESHOLD]
                [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE]
                [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE] [--min_split_read_size MIN_SPLIT_READ_SIZE]
                [-h] [--version]

Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and splitting reads with
internal adapters

Main options:
  -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: 16)

Barcode binning settings:
  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 (default: trim the reads)
  --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 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)

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 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)

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 in the middle)
  --discard_middle                      Reads with middle adapters will be discarded (default: reads with middle
                                        adapters are split) (required for reads to be used with Nanopolish, 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: 90.0)
  --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)

Help:
  -h, --help                            Show this help message and exit
  --version                             Show program's version number and exit