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.