Usage: cutadapt [options] <FASTA/FASTQ FILE> [<QUALITY FILE>]

Reads a FASTA or FASTQ file, finds and removes adapters, and writes the changed sequence to standard output. When finished, statistics are printed to standard error.

Use a dash "-" as file name to read from standard input (FASTA/FASTQ is autodetected).

If two file names are given, the first must be a .fasta or .csfasta file and the second must be a .qual file. This is the file format used by some 454 software and by the SOLiD sequencer. If you have color space data, you still need to provide the -c option to correctly deal with color space!

If the name of any input or output file ends with '.gz', it is assumed to be gzip-compressed.

If you want to search for the reverse complement of an adapter, you must provide an additional adapter sequence using another -a, -b or -g parameter.

If the input sequences are in color space, the adapter can be given in either color space (as a string of digits 0, 1, 2, 3) or in nucleotide space.

EXAMPLE

Assuming your sequencing data is available as a FASTQ file, use this command line: $ cutadapt -e ERROR-RATE -a ADAPTER-SEQUENCE input.fastq > output.fastq

See the README file for more help and examples.

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. All of the given adapters will be searched for in each read, but only the best matching one will be trimmed (but see the --times option).

-a ADAPTER, --adapter=ADAPTER

Sequence of an adapter that was ligated to the 3' end. The adapter itself and anything that follows 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.

-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.}

-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)

-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 'N's in the read as matches to the adapter (default: False).

-N, --no-match-adapter-wildcards

Do not treat 'N' in the adapter sequence as wildcards. This is needed when you want to search for literal 'N' characters.

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!

-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).

Options that influence what gets output to where:

-o FILE, --output=FILE

Write the modified sequences to this file instead of standard output and send the summary report to standard output. The format is FASTQ if qualities are available, FASTA otherwise. (default: standard output)

-r FILE, --rest-file=FILE

When the adapter matches in the middle of a read, write the rest (after the adapter) into a file. Use - for standard output.

--wildcard-file=FILE

When the adapter has wildcard bases ('N's) write adapter bases matching wildcard positions to FILE. Use - for standard output.

--too-short-output=FILE

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

--untrimmed-output=FILE

Write reads that do not contain the adapter to FILE, instead of writing them to the regular output file. (default: output to same file as trimmed)

Additional modifications to the reads:

-q CUTOFF, --quality-cutoff=CUTOFF

Trim low-quality ends from reads before adapter removal. The algorithm is the same as the one used by BWA (Subtract CUTOFF from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal) (default: none)

--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)

-x PREFIX, --prefix=PREFIX

Add this prefix to read names

-y SUFFIX, --suffix=SUFFIX

Add this suffix to read names

-c, --colorspace Colorspace mode: Also trim the color that is adjacent

to the found adapter.

-d, --double-encode

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

-t, --trim-primer When in color space, trim primer base and the first

color (which is the transition to the first nucleotide)

--strip-f3 For color space: Strip the _F3 suffix of read names --maq, --bwa MAQ- and BWA-compatible color space output. This

enables -c, -d, -t, --strip-f3, -y '/1' and -z.

--length-tag=TAG Search for TAG followed by a decimal number in the

name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'.

-z, --zero-cap Change negative quality values to zero (workaround to

avoid segmentation faults in BWA)

cutadapt: error: At least one parameter needed: name of a FASTA or FASTQ file.