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NAME

       cutadapt - manual page for cutadapt 1.8.3

DESCRIPTION

       cutadapt version 1.8.3 Copyright © 2010-2015 Marcel Martin <marcel.martin@scilifelab.se>

       cutadapt removes adapter sequences from high-throughput sequencing reads.

   Usage:
              cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq

   For paired-end reads:
              cutadapt  -a  ADAPT1  -A  ADAPT2  [options]  -o  out1.fastq -p out2.fastq in1.fastq
              in2.fastq

       Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC  wildcard  characters
       are  supported.  The  reverse  complement  is *not* automatically searched. All reads from
       input.fastq will be written to output.fastq with the  adapter  sequence  removed.  Adapter
       matching  is  error-tolerant.  Multiple  adapter  sequences  can  be given (use further -a
       options), but only the best-matching adapter will be removed.

       Input may also  be  in  FASTA  format.  Compressed  input  and  output  is  supported  and
       auto-detected  from  the  file  name  (.gz, .xz, .bz2). Use the file name '-' for standard
       input/output. Without the -o option, output is sent to standard output.

   Some other available features are:
              * Various other adapter  types  (5'  adapters,  "mixed"  5'/3'  adapters  etc.)   *
              Trimming  a  fixed number of bases * Quality trimming * Trimming colorspace reads *
              Filtering reads by various criteria

       Use    "cutadapt     --help"     to     see     all     command-line     options.      See
       http://cutadapt.readthedocs.org/ for full documentation.

OPTIONS

       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

       -f FORMAT, --format=FORMAT
              Input  file  format;  can  be  either 'fasta', 'fastq' or 'sra-fastq'. Ignored when
              reading csfasta/qual files (default: auto-detect from file name extension).

              Options that influence how the adapters are found:

              Each of the following three parameters (-a, -b, -g) can be used multiple times  and
              in  any  combination  to search for an entire set of adapters of possibly different
              types. Only the best matching adapter is  trimmed  from  each  read  (but  see  the
              --times  option).  Instead  of  giving  an  adapter  directly,  you  can also write
              file:FILE and the adapter sequences will be read from the given FILE (which must be
              in FASTA format).

       -a ADAPTER, --adapter=ADAPTER
              Sequence  of  an  adapter  that  was ligated to the 3' end.  The adapter itself and
              anything that follows is trimmed.  If  the  adapter  sequence  ends  with  the  '$'
              character, the adapter is anchored to the end of the read and only found if it is a
              suffix of the read.

       -g ADAPTER, --front=ADAPTER
              Sequence of an adapter that was ligated to the 5' end.   If  the  adapter  sequence
              starts  with the character '^', the adapter is 'anchored'. An anchored adapter must
              appear in its entirety at the 5' end of the read (it is a prefix of  the  read).  A
              non-anchored adapter may appear partially at the 5' end, or it may occur within the
              read. If it is found within a read, the sequence  preceding  the  adapter  is  also
              trimmed. In all cases, the adapter itself is trimmed.

       -b ADAPTER, --anywhere=ADAPTER
              Sequence  of  an  adapter  that  was ligated to the 5' or 3' end. If the adapter is
              found within the read or overlapping the 3' end of the read, the  behavior  is  the
              same  as  for  the  -a option. If the adapter overlaps the 5' end (beginning of the
              read), the initial portion of  the  read  matching  the  adapter  is  trimmed,  but
              anything that follows is kept.

       -e ERROR_RATE, --error-rate=ERROR_RATE
              Maximum  allowed  error  rate  (no. of errors divided by the length of the matching
              region) (default: 0.1)

       --no-indels
              Do not allow indels in the  alignments  (allow  only  mismatches).  Currently  only
              supported for anchored adapters. (default: allow both mismatches and indels)

       -n COUNT, --times=COUNT
              Try  to  remove  adapters at most COUNT times. Useful when an adapter gets appended
              multiple times (default: 1).

       -O LENGTH, --overlap=LENGTH
              Minimum overlap length. If the overlap between the read and the adapter is  shorter
              than LENGTH, the read is not modified. This reduces the no. of bases trimmed purely
              due to short random adapter matches (default: 3).

       --match-read-wildcards
              Allow IUPAC wildcards in reads (default: False).

       -N, --no-match-adapter-wildcards
              Do not interpret IUPAC wildcards in adapters.

              Options for filtering of processed reads:

       --discard-trimmed, --discard
              Discard reads that contain the adapter instead of trimming them.  Also  use  -O  in
              order to avoid throwing away too many randomly matching reads!

       --discard-untrimmed, --trimmed-only
              Discard reads that do not contain the adapter.

       -m LENGTH, --minimum-length=LENGTH
              Discard  trimmed reads that are shorter than LENGTH.  Reads that are too short even
              before adapter removal are also discarded. In colorspace, an initial primer is  not
              counted (default: 0).

       -M LENGTH, --maximum-length=LENGTH
              Discard  trimmed  reads  that are longer than LENGTH.  Reads that are too long even
              before adapter removal are also discarded. In colorspace, an initial primer is  not
              counted (default: no limit).

       --no-trim
              Match  and  redirect  reads  to output/untrimmed-output as usual, but do not remove
              adapters.

       --max-n=LENGTH
              The max proportion of N's allowed in a read. A number < 1  will  be  treated  as  a
              proportion  while  a  number  >  1  will  be  treated  as the maximum number of N's
              contained.

       --mask-adapter
              Mask adapters with 'N' characters instead of trimming them.

              Options that influence what gets output to where:

       --quiet
              Do not print a report at the end.

       -o FILE, --output=FILE
              Write modified reads to FILE. FASTQ or FASTA format is chosen depending  on  input.
              The  summary report is sent to standard output. Use '{name}' in FILE to demultiplex
              reads into multiple files. (default: trimmed reads are written to standard output)

       --info-file=FILE
              Write information about each read and  its  adapter  matches  into  FILE.  See  the
              documentation for the file format.

       -r FILE, --rest-file=FILE
              When  the  adapter  matches  in  the  middle  of  a read, write the rest (after the
              adapter) into FILE.

       --wildcard-file=FILE
              When the adapter has wildcard bases ('N's), write adapter bases  matching  wildcard
              positions  to FILE.  When there are indels in the alignment, this will often not be
              accurate.

       --too-short-output=FILE
              Write reads that are too short (according to  length  specified  by  -m)  to  FILE.
              (default: discard reads)

       --too-long-output=FILE
              Write  reads  that  are  too  long  (according  to length specified by -M) to FILE.
              (default: discard reads)

       --untrimmed-output=FILE
              Write reads that do not contain the adapter to FILE.  (default: output to same file
              as trimmed reads)

              Additional modifications to the reads:

       -u LENGTH, --cut=LENGTH
              Remove  LENGTH bases from the beginning or end of each read. If LENGTH is positive,
              the bases are removed from the beginning of each read. If LENGTH is  negative,  the
              bases  are removed from the end of each read. This option can be specified twice if
              the LENGTHs have different signs.

       -q [5'CUTOFF,]3'CUTOFF, --quality-cutoff=[5'CUTOFF,]3'CUTOFF
              Trim low-quality bases from 5' and/or 3' ends of reads before adapter  removal.  If
              one  value is given, only the 3' end is trimmed. If two comma-separated cutoffs are
              given, the 5' end is trimmed with the first cutoff, the 3' end with the second. The
              algorithm  is  the  same  as the one used by BWA (see documentation).  (default: no
              trimming)

       --quality-base=QUALITY_BASE
              Assume that quality values  are  encoded  as  ascii(quality  +  QUALITY_BASE).  The
              default  (33) is usually correct, except for reads produced by some versions of the
              Illumina pipeline, where this should be set to 64. (Default: 33)

       --trim-n
              Trim N's on ends of reads.

       -x PREFIX, --prefix=PREFIX
              Add this prefix to read names

       -y SUFFIX, --suffix=SUFFIX
              Add this suffix to read names

       --strip-suffix=STRIP_SUFFIX
              Remove this suffix from read names if present. Can be given multiple times.

       -c, --colorspace
              Colorspace mode: Also trim the color that is adjacent to the found adapter.

       -d, --double-encode
              When in colorspace, double-encode colors (map 0,1,2,3,4 to A,C,G,T,N).

       -t, --trim-primer
              When in colorspace, trim primer base and the first color (which is  the  transition
              to the first nucleotide)

       --strip-f3
              For colorspace: Strip the _F3 suffix of read names

       --maq, --bwa
              MAQ-  and BWA-compatible colorspace output. This enables -c, -d, -t, --strip-f3 and
              -y '/1'.

       --length-tag=TAG
              Search for TAG followed by a decimal number in the description field of  the  read.
              Replace  the  decimal  number  with  the  correct  length of the trimmed read.  For
              example, use --length-tag 'length=' to correct fields like 'length=123'.

       --no-zero-cap
              Do not change negative quality values to zero.  Colorspace  quality  values  of  -1
              would  appear  as  spaces  in the output FASTQ file. Since many tools have problems
              with that, negative qualities are converted to zero when trimming colorspace  data.
              Use this option to keep negative qualities.

       -z, --zero-cap
              Change   negative  quality  values  to  zero.  This  is  enabled  by  default  when
              -c/--colorspace is also enabled. Use the above option to disable it.

              Paired-end options.:

              The -A/-G/-B/-U options work like their -a/-b/-g/-u counterparts.

       -A ADAPTER
              3' adapter to be removed from the second read in a pair.

       -G ADAPTER
              5' adapter to be removed from the second read in a pair.

       -B ADAPTER
              5'/3 adapter to be removed from the second read in a pair.

       -U LENGTH
              Remove LENGTH bases from the beginning or end of each read (see --cut).

       -p FILE, --paired-output=FILE
              Write second read in a pair to FILE.

       --untrimmed-paired-output=FILE
              Write the second read in a pair to this FILE when no adapter was found in the first
              read.  Use  this  option  together  with --untrimmed-output when trimming pairedend
              reads. (Default: output to same file as trimmed reads.)

SEE ALSO

       The full documentation for cutadapt is maintained as a Texinfo manual.  If  the  info  and
       cutadapt programs are properly installed at your site, the command

              info cutadapt

       should give you access to the complete manual.