qiime deblur denoise-other (version 2019.4)

--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]:

--i-reference-seqs: ARTIFACT FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences. [required]:

--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]:

--p-left-trim-len: INTEGER Range(0, None) Sequence trimming from the 5' end. A value of 0 will disable this trim. [default: 0]:

--p-sample-stats: --p-no-sample-stats If true, gather stats per sample. [default: False]:

--p-mean-error: NUMBER The mean per nucleotide error, used for original sequence estimate. [default: 0.005]:

--p-indel-prob: NUMBER Insertion/deletion (indel) probability (same for N indels). [default: 0.01]:

--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]:

--p-min-reads: INTEGER Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]:

--p-min-size: INTEGER In each sample, discard all features with an abundance less than min-size. [default: 2]:

--p-no-hashed-feature-ids: If false, hash the feature IDs. [default: False]:

Deblur sequences using a user-specified positive filter.

Perform sequence quality control for Illumina data using the Deblur workflow, including positive alignment-based filtering. Only forward reads are supported at this time. This mode of execution is particularly useful when operating on non-16S data. For example, to apply Deblur to 18S data, you would want to specify a reference composed of 18S sequences in order to filter out sequences which do not appear to be 18S. The assessment is performed by local alignment using SortMeRNA with a permissive e-value threshold.

Parameters

demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]: The demultiplexed sequences to be denoised.
reference_seqs : FeatureData[Sequence]: Positive filtering database. Keep all sequences aligning to these sequences.
trim_length : Int: Sequence trim length, specify -1 to disable trimming.
left_trim_len : Int % Range(0, None), optional: Sequence trimming from the 5' end. A value of 0 will disable this trim.
sample_stats : Bool, optional: If true, gather stats per sample.
mean_error : Float, optional: The mean per nucleotide error, used for original sequence estimate.
indel_prob : Float, optional: Insertion/deletion (indel) probability (same for N indels).
indel_max : Int, optional: Maximum number of insertion/deletions.
min_reads : Int, optional: Retain only features appearing at least min_reads times across all samples in the resulting feature table.
min_size : Int, optional: In each sample, discard all features with an abundance less than min_size.
hashed_feature_ids : Bool, optional: If true, hash the feature IDs.

Returns

table : FeatureTable[Frequency]: The resulting denoised feature table.
representative_sequences : FeatureData[Sequence]: The resulting feature sequences.
stats : DeblurStats: Per-sample stats if requested.