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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