qiime vsearch join-pairs (version 2019.4)

--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]:

--p-truncqual: INTEGER Truncate sequences at the first base with the Range(0, None) specified quality score value or lower. [optional]:

--p-minlen: INTEGER Sequences shorter than minlen after truncation are Range(0, None) discarded. [default: 1]:

--p-maxns: INTEGER Sequences with more than maxns N characters are Range(0, None) discarded. [optional]:

--p-allowmergestagger: --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]:

--p-minovlen: INTEGER Minimum overlap length of forward and reverse reads Range(0, None) for joining. [default: 10]:

--p-maxdiffs: INTEGER Maximum number of mismatches in the forward/reverse Range(0, None) read overlap for joining. [default: 10]:

--p-minmergelen: INTEGER Range(0, None) Minimum length of the joined read to be retained. [optional]:

--p-maxmergelen: INTEGER Range(0, None) Maximum length of the joined read to be retained. [optional]:

--p-maxee: NUMBER Maximum number of expected errors in the joined read Range(0.0, None) to be retained. [optional]:

--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]:

--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]:

--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]:

--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]:

Join paired-end reads.

Join paired-end sequence reads using vsearch's merge_pairs function. The qmin, qminout, qmax, and qmaxout parameters should only need to be modified when working with older fastq sequence data. See the vsearch documentation for details on how paired-end joining is performed, and for more information on the parameters to this method.

Parameters

demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]: The demultiplexed paired-end sequences to be joined.
truncqual : Int % Range(0, None), optional: Truncate sequences at the first base with the specified quality score value or lower.
minlen : Int % Range(0, None), optional: Sequences shorter than minlen after truncation are discarded.
maxns : Int % Range(0, None), optional: Sequences with more than maxns N characters are discarded.
allowmergestagger : Bool, optional: Allow joining of staggered read pairs.
minovlen : Int % Range(0, None), optional: Minimum overlap length of forward and reverse reads for joining.
maxdiffs : Int % Range(0, None), optional: Maximum number of mismatches in the forward/reverse read overlap for joining.
minmergelen : Int % Range(0, None), optional: Minimum length of the joined read to be retained.
maxmergelen : Int % Range(0, None), optional: Maximum length of the joined read to be retained.
maxee : Float % Range(0.0, None), optional: Maximum number of expected errors in the joined read to be retained.
qmin : Int % Range(-5, 2, inclusive_end=True), optional: The minimum allowed quality score in the input.
qminout : Int % Range(-5, 2, inclusive_end=True), optional: The minimum allowed quality score to use in output.
qmax : Int % Range(40, 41, inclusive_end=True), optional: The maximum allowed quality score in the input.
qmaxout : Int % Range(40, 41, inclusive_end=True), optional: The maximum allowed quality score to use in output.

Returns

joined_sequences : SampleData[JoinedSequencesWithQuality]: The joined sequences.