qiime_feature-classifier_extract-reads.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.

qiime feature-classifier extract-reads (version 2019.4)

--p-f-primer: TEXT forward primer sequence [required]:

--p-r-primer: TEXT reverse primer sequence [required]:

--p-trunc-len: INTEGER read is cut to trunc-len if trunc-len is positive. Applied before trim-left. [default: 0]:

--p-trim-left: INTEGER trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trunc-len. [default: 0]:

--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]:

--p-min-length: INTEGER Minimum amplicon length. Shorter amplicons are Range(0, None) discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering. [default: 50]:

--p-max-length: INTEGER Maximum amplicon length. Longer amplicons are Range(0, None) discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering. [default: 0]:

Extract reads from reference

Extract sequencing-like reads from a reference database.

Parameters

sequences : FeatureData[Sequence]
f_primer : Str: forward primer sequence
r_primer : Str: reverse primer sequence
trunc_len : Int, optional: read is cut to trunc_len if trunc_len is positive. Applied before trim_left.
trim_left : Int, optional: trim_left nucleotides are removed from the 5' end if trim_left is positive. Applied after trunc_len.
identity : Float, optional: minimum combined primer match identity threshold.
min_length : Int % Range(0, None), optional: Minimum amplicon length. Shorter amplicons are discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering.
max_length : Int % Range(0, None), optional: Maximum amplicon length. Longer amplicons are discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering.

Returns

reads : FeatureData[Sequence]