q2-quality-filter

This QIIME 2 plugin supports filtering and trimming of sequence reads based on PHRED scores and ambiguous nucleotide characters.

version: 2024.10.0

website: https://github.com/qiime2/q2-quality-filter

user support:

Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

citations:

Bokulich et al., 2013

Actions¶

Artifact Classes¶

Formats¶

quality-filter q-score¶

This method filters sequence based on quality scores and the presence of ambiguous base calls.

Citations¶

Bokulich et al., 2013

Inputs¶

demux: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] | SampleData[JoinedSequencesWithQuality]

The demultiplexed sequence data to be quality filtered.[required]

Parameters¶

min_quality: Int

The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores.[default: 4]

quality_window: Int

The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read.[default: 3]

min_length_fraction: Float

The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length.[default: 0.75]

max_ambiguous: Int

The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on min_length_fraction.[default: 0]

Outputs¶

filtered_sequences: SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]

The resulting quality-filtered sequences.[required]

filter_stats: QualityFilterStats

Summary statistics of the filtering process.[required]

Examples¶

q_score¶

wget -O 'demuxed-seqs.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/quality-filter/q-score/1/demuxed-seqs.qza'

qiime quality-filter q-score \
  --i-demux demuxed-seqs.qza \
  --o-filtered-sequences dumux-filtered.qza \
  --o-filter-stats demux-filter-stats.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.quality_filter.actions as quality_filter_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/quality-filter/q-score/1/demuxed-seqs.qza'
fn = 'demuxed-seqs.qza'
request.urlretrieve(url, fn)
demuxed_seqs = Artifact.load(fn)

dumux_filtered, demux_filter_stats = quality_filter_actions.q_score(
    demux=demuxed_seqs,
)

library(reticulate)

Artifact <- import("qiime2")$Artifact
quality_filter_actions <- import("qiime2.plugins.quality_filter.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/quality-filter/q-score/1/demuxed-seqs.qza'
fn <- 'demuxed-seqs.qza'
request$urlretrieve(url, fn)
demuxed_seqs <- Artifact$load(fn)

action_results <- quality_filter_actions$q_score(
    demux=demuxed_seqs,
)
dumux_filtered <- action_results$filtered_sequences
demux_filter_stats <- action_results$filter_stats

from q2_quality_filter._examples import q_score_example

q_score_example(use)