q2-long-reads-qc

QIIME2 plugin that utilizes Chopper and NanoPlot for quality control analysis of long sequences, generating easy-to-interpret stats as QIIME2 vizualization and allows trimming based on various filters.

Installation¶

We provide three options for installing q2-long-reads-qc via conda environment files, depending on your preferred QIIME2 distribution. The environment files can be found in the environment-files/ directory of this repository:

1: Tiny distribution¶

Use the environment file q2-long-reads-qc-qiime2-tiny-2025.10.yml to create a new conda environment based on the tiny distro.

conda env create -n long-reads-env -f q2-long-reads-qc-qiime2-tiny-2025.10.yml
conda activate q2-long-reads-tiny

2: Amplicon distribution¶

Use the environment file q2-long-reads-qc-qiime2-amplicon-2025.10.yml to create a new conda environment.

conda env create -n long-reads-env -f q2-long-reads-qc-qiime2-amplicon-2025.10.yml
conda activate q2-long-reads-amplicon

3: Moshpit distribution¶

Use the environment file q2-long-reads-qc-qiime2-moshpit-2025.10.yml to create a new conda environment based on the moshpit distro.

conda env create -n long-reads-env -f q2-long-reads-qc-qiime2-moshpit-2025.10.yml
conda activate q2-long-reads-moshpit

Execute¶

trime-single¶

Trim 20 nucleotides from the start of each read¶

qiime long-reads-qc trim --i-query-reads reads.qza --p-headcrop 20 --verbose --o-filtered-query-reads filtered.qza

stat¶

Generate a visualization of statistics for the input sequences¶

qiime long-reads-qc stats --i-sequences paired_reads.qza --o-visualization viz.qzv

Qiime2 view can be used to view the result visualization¶

We have added a new semantic type for the cutadapt log files named “CutadaptLogs”.

qiime tools import --type 'CutadaptLogs' --input-path dir_with_cutadapt_log_files --output-path cutadapt_logs.qza