Docstring:
Usage: qiime vsearch merge-pairs [OPTIONS]
Merge paired-end sequence reads using vsearch's merge_pairs function. See
the vsearch documentation for details on how paired-end merging is
performed, and for more information on the parameters to this method.
Inputs:
--i-demultiplexed-seqs ARTIFACT SampleData[PairedEndSequencesWithQuality]
The demultiplexed paired-end sequences to be merged.
[required]
Parameters:
--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 merging of staggered read pairs.
[default: False]
--p-minovlen INTEGER Minimum length of the area of overlap between reads
Range(5, None) during merging. [default: 10]
--p-maxdiffs INTEGER Maximum number of mismatches in the area of overlap
Range(0, None) during merging. [default: 10]
--p-minmergelen INTEGER
Range(0, None) Minimum length of the merged read to be retained.
[optional]
--p-maxmergelen INTEGER
Range(0, None) Maximum length of the merged read to be retained.
[optional]
--p-maxee NUMBER Maximum number of expected errors in the merged read
Range(0.0, None) to be retained. [optional]
--p-threads NTHREADS The number of threads to use for computation. Does
not scale much past 4 threads. [default: 1]
Outputs:
--o-merged-sequences ARTIFACT SampleData[JoinedSequencesWithQuality]
The merged sequences. [required]
--o-unmerged-sequences ARTIFACT SampleData[PairedEndSequencesWithQuality]
The unmerged paired-end reads. [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--help Show this message and exit.
Import:
from qiime2.plugins.vsearch.methods import merge_pairs
Docstring:
Merge paired-end reads.
Merge paired-end sequence reads using vsearch's merge_pairs function. See
the vsearch documentation for details on how paired-end merging is
performed, and for more information on the parameters to this method.
Parameters
----------
demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
The demultiplexed paired-end sequences to be merged.
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 merging of staggered read pairs.
minovlen : Int % Range(5, None), optional
Minimum length of the area of overlap between reads during merging.
maxdiffs : Int % Range(0, None), optional
Maximum number of mismatches in the area of overlap during merging.
minmergelen : Int % Range(0, None), optional
Minimum length of the merged read to be retained.
maxmergelen : Int % Range(0, None), optional
Maximum length of the merged read to be retained.
maxee : Float % Range(0.0, None), optional
Maximum number of expected errors in the merged read to be retained.
threads : Threads, optional
The number of threads to use for computation. Does not scale much past
4 threads.
Returns
-------
merged_sequences : SampleData[JoinedSequencesWithQuality]
The merged sequences.
unmerged_sequences : SampleData[PairedEndSequencesWithQuality]
The unmerged paired-end reads.
