cutadapt

RNA-seq

scRNA-seq

high-throughput

Description

Cutadapt removes adapter sequences from high-throughput sequencing reads.

Type

bash_script

License

MIT

Keywords

RNA-seq

scRNA-seq

high-throughput

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output._*.fast[a,q]"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/cutadapt/main.nf \  
  -params-file params.yaml

Specify Adapters for R1

Name	Type & Properties	Description
--adapter -a	string multiple	Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read.
--front -g	string multiple	Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read.
--anywhere -b	string multiple	Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under -a and -g are allowed. If the first base of the read is part of the match, the behavior is as with -g, otherwise as with -a. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!

Name

Type & Properties

--adapter

-a

string

multiple

--front

-g

string

multiple

--anywhere

-b

string

multiple

Specify Adapters using Fasta files for R1

Name	Type & Properties	Description
--adapter_fasta	file multiple	Fasta file containing sequences of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read.
--front_fasta	file	Fasta file containing sequences of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read.
--anywhere_fasta	file	Fasta file containing sequences of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under -a and -g are allowed. If the first base of the read is part of the match, the behavior is as with -g, otherwise as with -a. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!

Name

Type & Properties

--adapter_fasta

file

multiple

--front_fasta

file

--anywhere_fasta

file

Specify Adapters for R2

Name	Type & Properties	Description
--adapter_r2 -A	string multiple	Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read.
--front_r2 -G	string multiple	Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read.
--anywhere_r2 -B	string multiple	Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under -a and -g are allowed. If the first base of the read is part of the match, the behavior is as with -g, otherwise as with -a. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!

Name

Type & Properties

--adapter_r2

-A

string

multiple

--front_r2

-G

string

multiple

--anywhere_r2

-B

string

multiple

Specify Adapters using Fasta files for R2

Name	Type & Properties	Description
--adapter_r2_fasta	file	Fasta file containing sequences of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read.
--front_r2_fasta	file	Fasta file containing sequences of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read.
--anywhere_r2_fasta	file	Fasta file containing sequences of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under -a and -g are allowed. If the first base of the read is part of the match, the behavior is as with -g, otherwise as with -a. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!

Name

Type & Properties

--adapter_r2_fasta

file

--front_r2_fasta

file

--anywhere_r2_fasta

file

Paired-end options

Name	Type & Properties	Description
--pair_adapters	boolean_true	Treat adapters given with -a/-A etc. as pairs. Either both or none are removed from each read pair.
--pair_filter	string	Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered.
--interleaved	boolean_true	Read and/or write interleaved paired-end reads.

Name

Type & Properties

--pair_adapters

boolean_true

--pair_filter

string

--interleaved

boolean_true

Input parameters

Name	Type & Properties	Description
--input	file required	Input fastq file for single-end reads or R1 for paired-end reads.
--input_r2	file	Input fastq file for R2 in the case of paired-end reads.
--error_rate -E --errors	double	Maximum allowed error rate (if 0 <= E < 1), or absolute number of errors for full-length adapter match (if E is an integer >= 1). Error rate = no. of errors divided by length of matching region. Default: 0.1 (10%).
--no_indels	boolean_true	Allow only mismatches in alignments.
--times -n	integer	Remove up to COUNT adapters from each read. Default: 1.
--overlap -O	integer	Require MINLENGTH overlap between read and adapter for an adapter to be found. The default is 3.
--match_read_wildcards	boolean_true	Interpret IUPAC wildcards in reads.
--no_match_adapter_wildcards	boolean_true	Do not interpret IUPAC wildcards in adapters.
--action	string	What to do if a match was found. trim: trim adapter and up- or downstream sequence; retain: trim, but retain adapter; mask: replace with 'N' characters; lowercase: convert to lowercase; none: leave unchanged. The default is trim.
--revcomp --rc	boolean_true	Check both the read and its reverse complement for adapter matches. If match is on reverse-complemented version, output that one.

Name

Type & Properties

--input

file

required

--input_r2

file

--error_rate

-E

--errors

double

--no_indels

boolean_true

--times

-n

integer

--overlap

-O

integer

--match_read_wildcards

boolean_true

--no_match_adapter_wildcards

boolean_true

--action

string

--revcomp

--rc

boolean_true

Demultiplexing options

Name	Type & Properties	Description
--demultiplex_mode	string	Enable demultiplexing and set the mode for it. With mode 'unique_dual', adapters from the first and second read are used, and the indexes from the reads are only used in pairs. This implies --pair_adapters. Enabling mode 'combinatorial_dual' allows all combinations of the sets of indexes on R1 and R2. It is necessary to write each read pair to an output file depending on the adapters found on both R1 and R2. Mode 'single', uses indexes or barcodes located at the 5' end of the R1 read (single).

Name

Type & Properties

--demultiplex_mode

string

Read modifications

Name	Type & Properties	Description
--cut -u	integer multiple	Remove LEN bases from each read (or R1 if paired; use --cut_r2 option for R2). If LEN is positive, remove bases from the beginning. If LEN is negative, remove bases from the end. Can be used twice if LENs have different signs. Applied before adapter trimming.
--cut_r2	integer multiple	Remove LEN bases from each read (for R2). If LEN is positive, remove bases from the beginning. If LEN is negative, remove bases from the end. Can be used twice if LENs have different signs. Applied before adapter trimming.
--nextseq_trim	string	NextSeq-specific quality trimming (each read). Trims also dark cycles appearing as high-quality G bases.
--quality_cutoff -q	string	Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. 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.
--quality_cutoff_r2 -Q	string	Quality-trimming cutoff for R2. Default: same as for R1
--quality_base	integer	Assume that quality values in FASTQ are encoded as ascii(quality + N). This needs to be set to 64 for some old Illumina FASTQ files. The default is 33.
--poly_a	boolean_true	Trim poly-A tails
--length -l	integer	Shorten reads to LENGTH. Positive values remove bases at the end while negative ones remove bases at the beginning. This and the following modifications are applied after adapter trimming.
--trim_n	boolean_true	Trim N's on ends of reads.
--length_tag	string	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'.
--strip_suffix	string	Remove this suffix from read names if present. Can be given multiple times.
--prefix -x	string	Add this prefix to read names. Use {name} to insert the name of the matching adapter.
--suffix -y	string	Add this suffix to read names; can also include {name}
--rename	string	Rename reads using TEMPLATE containing variables such as {id}, {adapter_name} etc. (see documentation)
--zero_cap -z	boolean_true	Change negative quality values to zero.

Name

Type & Properties

--cut

-u

integer

multiple

--cut_r2

integer

multiple

--nextseq_trim

string

--quality_cutoff

-q

string

--quality_cutoff_r2

-Q

string

--quality_base

integer

--poly_a

boolean_true

--length

-l

integer

--trim_n

boolean_true

--length_tag

string

--strip_suffix

string

--prefix

-x

string

--suffix

-y

string

--rename

string

--zero_cap

-z

boolean_true

Filtering of processed reads

Name	Type & Properties	Description
--minimum_length -m	string	Discard reads shorter than LEN. Default is 0. When trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately by separating them with a colon (:). If the colon syntax is not used, the same minimum length applies to both reads, as discussed above. Also, one of the values can be omitted to impose no restrictions. For example, with -m 17:, the length of R1 must be at least 17, but the length of R2 is ignored.
--maximum_length -M	string	Discard reads longer than LEN. Default: no limit. For paired reads, see the remark for --minimum_length
--max_n	string	Discard reads with more than COUNT 'N' bases. If COUNT is a number between 0 and 1, it is interpreted as a fraction of the read length.
--max_expected_errors --max_ee	long	Discard reads whose expected number of errors (computed from quality values) exceeds ERRORS.
--max_average_error_rate --max_aer	long	as --max_expected_errors (see above), but divided by length to account for reads of varying length.
--discard_trimmed --discard	boolean_true	Discard reads that contain an adapter. Use also -O to avoid discarding too many randomly matching reads.
--discard_untrimmed --trimmed_only	boolean_true	Discard reads that do not contain an adapter.
--discard_casava	boolean_true	Discard reads that did not pass CASAVA filtering (header has :Y:).

Name

Type & Properties

--minimum_length

-m

string

--maximum_length

-M

string

--max_n

string

--max_expected_errors

--max_ee

long

--max_average_error_rate

--max_aer

long

--discard_trimmed

--discard

boolean_true

--discard_untrimmed

--trimmed_only

boolean_true

--discard_casava

boolean_true

Output parameters

Name	Type & Properties	Description
--report	string	Which type of report to print: 'full' (default) or 'minimal'.
--json	boolean_true	Write report in JSON format to this file.
--output	file required multiple output	Glob pattern for matching the expected output files. Should include `$output_dir`.
--fasta	boolean_true	Output FASTA to standard output even on FASTQ input.
--info_file	boolean_true	Write information about each read and its adapter matches into info.txt in the output directory. See the documentation for the file format.

Name

Type & Properties

--report

string

--json

boolean_true

--output

file

required

multiple

output

--fasta

boolean_true

--info_file

boolean_true

Debug

Name	Type & Properties	Description
--debug	boolean_true	Print debug information

Name

Type & Properties

--debug

boolean_true