Docstring:
Usage: qiime quality-control filter-reads [OPTIONS]
Filter out (or keep) demultiplexed single- or paired-end sequences that
align to a reference database, using bowtie2 and samtools. This method can
be used to filter out human DNA sequences and other contaminants in any
FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or
alternatively (when exclude_seqs is False) to only keep sequences that do
align to the reference.
Inputs:
--i-demultiplexed-sequences ARTIFACT SampleData[SequencesWithQuality¹ |
PairedEndSequencesWithQuality²]
The sequences to be trimmed. [required]
--i-database ARTIFACT Bowtie2 indexed database.
Bowtie2Index [required]
Parameters:
--p-n-threads NTHREADS Number of alignment threads to launch. [default: 1]
--p-mode TEXT Choices('local', 'global')
Bowtie2 alignment settings. See bowtie2 manual for
more details. [default: 'local']
--p-sensitivity TEXT Choices('very-fast', 'fast', 'sensitive',
'very-sensitive') Bowtie2 alignment sensitivity. See bowtie2 manual
for details. [default: 'sensitive']
--p-ref-gap-open-penalty INTEGER
Range(1, None) Reference gap open penalty. [default: 5]
--p-ref-gap-ext-penalty INTEGER
Range(1, None) Reference gap extend penalty. [default: 3]
--p-exclude-seqs / --p-no-exclude-seqs
Exclude sequences that align to reference. Set this
option to False to exclude sequences that do not
align to the reference database. [default: True]
Outputs:
--o-filtered-sequences ARTIFACT SampleData[SequencesWithQuality¹ |
PairedEndSequencesWithQuality²]
The resulting filtered sequences. [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.quality_control.methods import filter_reads
Docstring:
Filter demultiplexed sequences by alignment to reference database.
Filter out (or keep) demultiplexed single- or paired-end sequences that
align to a reference database, using bowtie2 and samtools. This method can
be used to filter out human DNA sequences and other contaminants in any
FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or
alternatively (when exclude_seqs is False) to only keep sequences that do
align to the reference.
Parameters
----------
demultiplexed_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
The sequences to be trimmed.
database : Bowtie2Index
Bowtie2 indexed database.
n_threads : Threads, optional
Number of alignment threads to launch.
mode : Str % Choices('local', 'global'), optional
Bowtie2 alignment settings. See bowtie2 manual for more details.
sensitivity : Str % Choices('very-fast', 'fast', 'sensitive', 'very-sensitive'), optional
Bowtie2 alignment sensitivity. See bowtie2 manual for details.
ref_gap_open_penalty : Int % Range(1, None), optional
Reference gap open penalty.
ref_gap_ext_penalty : Int % Range(1, None), optional
Reference gap extend penalty.
exclude_seqs : Bool, optional
Exclude sequences that align to reference. Set this option to False to
exclude sequences that do not align to the reference database.
Returns
-------
filtered_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
The resulting filtered sequences.
