.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH PORECHOP "1" "August 2018" "porechop 0.2.3" "User Commands"
.SH NAME
porechop \- adapter trimmer for Oxford Nanopore reads
.SH SYNOPSIS
.B porechop
[\-h] \fB\-i\fR 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]
.SH DESCRIPTION
Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them
from the ends and splitting reads with internal adapters
.SH OPTIONS
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "Main options:"
.TP
\fB\-i\fR INPUT, \fB\-\-input\fR INPUT
FASTA/FASTQ of input reads or a directory which will
be recursively searched for FASTQ files (required)
.TP
\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
Filename for FASTA or FASTQ of trimmed reads (if not
set, trimmed reads will be printed to stdout)
.TP
\fB\-\-format\fR {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)
.TP
\fB\-v\fR VERBOSITY, \fB\-\-verbosity\fR 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)
.TP
\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
Number of threads to use for adapter alignment
(default: 4)
.TP
\fB\-\-version\fR
show program's version number and exit
.SS "Barcode binning settings:"
.IP
Control the binning of reads based on barcodes (i.e. barcode
demultiplexing)
.TP
\fB\-b\fR BARCODE_DIR, \fB\-\-barcode_dir\fR BARCODE_DIR
Reads will be binned based on their barcode and
saved to separate files in this directory
(incompatible with \fB\-\-output\fR)
.TP
\fB\-\-barcode_threshold\fR BARCODE_THRESHOLD
A read must have at least this percent identity to a
barcode to be binned (default: 75.0)
.TP
\fB\-\-barcode_diff\fR 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)
.TP
\fB\-\-require_two_barcodes\fR
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)
.TP
\fB\-\-untrimmed\fR
Bin reads but do not trim them (appropriate if reads
are to be used with Nanopolish) (default: trim the
reads)
.TP
\fB\-\-discard_unassigned\fR
Discard unassigned reads (instead of creating a
"none" bin) (default: False)
.SS "Adapter search settings:"
.IP
Control how the program determines which adapter sets are present
.TP
\fB\-\-adapter_threshold\fR 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)
.TP
\fB\-\-check_reads\fR CHECK_READS
This many reads will be aligned to all possible
adapters to determine which adapter sets are present
(default: 10000)
.TP
\fB\-\-scoring_scheme\fR SCORING_SCHEME
Comma\-delimited string of alignment scores: match,
mismatch, gap open, gap extend (default: 3,\-6,\-5,\-2)
.SS "End adapter settings:"
.IP
Control the trimming of adapters from read ends
.TP
\fB\-\-end_size\fR END_SIZE
The number of base pairs at each end of the read
which will be searched for adapter sequences
(default: 150)
.TP
\fB\-\-min_trim_size\fR MIN_TRIM_SIZE
Adapter alignments smaller than this will be ignored
(default: 4)
.TP
\fB\-\-extra_end_trim\fR EXTRA_END_TRIM
This many additional bases will be removed next to
adapters found at the ends of reads (default: 2)
.TP
\fB\-\-end_threshold\fR END_THRESHOLD
Adapters at the ends of reads must have at least
this percent identity to be removed (0 to 100)
(default: 75.0)
.SS "Middle adapter settings:"
.IP
Control the splitting of read from middle adapters
.TP
\fB\-\-no_split\fR
Skip splitting reads based on middle adapters
(default: split reads when an adapter is found in
the middle)
.TP
\fB\-\-discard_middle\fR
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)
.TP
\fB\-\-middle_threshold\fR MIDDLE_THRESHOLD
Adapters in the middle of reads must have at least
this percent identity to be found (0 to 100)
(default: 85.0)
.TP
\fB\-\-extra_middle_trim_good_side\fR EXTRA_MIDDLE_TRIM_GOOD_SIDE
This many additional bases will be removed next to
middle adapters on their "good" side (default: 10)
.TP
\fB\-\-extra_middle_trim_bad_side\fR EXTRA_MIDDLE_TRIM_BAD_SIDE
This many additional bases will be removed next to
middle adapters on their "bad" side (default: 100)
.TP
\fB\-\-min_split_read_size\fR MIN_SPLIT_READ_SIZE
Post\-split read pieces smaller than this many base
pairs will not be outputted (default: 1000)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.