q2-sort-me-rna

Overview

q2-sort-me-rna is a plugin for QIIME 2, designed to seamlessly integrate with the SortMeRNA package. This plugin accepts all parameters listed in the SortMeRNA manual. Note that the formatting of the plugin parameters differs slightly; they are lowercased and use hyphenation, whereas SortMeRNA uses a mix of underscores and capitalization.

Limitations

• Input Format: SortMeRNA accepts sequence reads in both the FASTA and FASTQ formats. However, this plugin only accepts reads in the FASTQ format. For the reference database, it is perfectly fine to use FASTA.

• QIIME Types: QIIME types must be non-empty. During OTU mapping, it is possible for no elements to be mapped, and in this case, an exception will be thrown.

Examples

Set the location of the input and output artifacts. Ensure that these locations exist before proceeding.

sortmerna_work_dir = out
q2smr_output_dir = output
art_dir = ./q2_sort_me_rna/tests/assets
seq_dir = ./q2_sort_me_rna/tests/assets/seq

Align the Raw Reads

qiime sort-me-rna sort-rna \
--i-reads "$(art_dir)/raw_sequence.qza" \
--i-ref "$(art_dir)/rrna_references.qza"  \
--p-workdir "./$(q2smr_output_dir)" \
--output-dir "./$(q2smr_output_dir)/qiime-output" \
--verbose

Align the Raw Reads and Produce an OTU Mapping

qiime sort-me-rna otu-mapping \
--i-reads "$(art_dir)/raw_sequence.qza" \
--i-ref "$(art_dir)/rrna_references.qza"  \
--p-workdir "./$(q2smr_output_dir)" \
--p-id 0.12 \
--p-coverage 0.12 \
--output-dir "./$(q2smr_output_dir)/qiime-output" \
--verbose

Align the Raw Reads and Produce an OTU Mapping with Denovo Reads

qiime sort-me-rna denovo-otu-mapping \
--i-reads "$(art_dir)/raw_sequence.qza" \
--i-ref "$(art_dir)/rrna_references.qza"  \
--p-workdir "./$(q2smr_output_dir)" \
--p-id 0.7 \
--p-coverage 0.7 \
--output-dir "./$(q2smr_output_dir)/qiime-output" \
--verbose

Feel free to reach out if you have any questions or encounter issues. Happy sorting!