Description

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Options

*** Barcode binning settings ***

-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 the ends (appropriate if reads are to be
                                  used with Nanopolish) (default: False)

*** Adapter search settings ***

--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 ***

--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 ***

--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)