NAME

       porechop - adapter trimmer for Oxford Nanopore reads

SYNOPSIS

       porechop  [-h]  -i  INPUT  [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY] [-t
       THREADS]   [--version]   [-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]

DESCRIPTION

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

OPTIONS

   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 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

   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 (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)

   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) (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)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

porechop 0.2.3                                     August 2018                                       PORECHOP(1)