q2-feature-classifier

Formats¶

This QIIME 2 plugin supports taxonomic classification of features using a variety of methods, including Naive Bayes, vsearch, and BLAST+.

version: 2024.10.0
website: https://github.com/qiime2/q2-feature-classifier
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Bokulich et al., 2018

Actions¶

Name	Type	Short Description
fit-classifier-sklearn	method	Train an almost arbitrary scikit-learn classifier
classify-sklearn	method	Pre-fitted sklearn-based taxonomy classifier
fit-classifier-naive-bayes	method	Train the naive_bayes classifier
extract-reads	method	Extract reads from reference sequences.
find-consensus-annotation	method	Find consensus among multiple annotations.
makeblastdb	method	Make BLAST database.
blast	method	BLAST+ local alignment search.
vsearch-global	method	VSEARCH global alignment search
classify-consensus-blast	pipeline	BLAST+ consensus taxonomy classifier
classify-consensus-vsearch	pipeline	VSEARCH-based consensus taxonomy classifier
classify-hybrid-vsearch-sklearn	pipeline	ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier

Artifact Classes¶

Formats¶

This QIIME 2 plugin supports taxonomic classification of features using a variety of methods, including Naive Bayes, vsearch, and BLAST+.

version: 2024.10.0
website: https://github.com/qiime2/q2-feature-classifier
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Bokulich et al., 2018

Actions¶

Name	Type	Short Description
fit-classifier-sklearn	method	Train an almost arbitrary scikit-learn classifier
classify-sklearn	method	Pre-fitted sklearn-based taxonomy classifier
fit-classifier-naive-bayes	method	Train the naive_bayes classifier
extract-reads	method	Extract reads from reference sequences.
find-consensus-annotation	method	Find consensus among multiple annotations.
makeblastdb	method	Make BLAST database.
blast	method	BLAST+ local alignment search.
vsearch-global	method	VSEARCH global alignment search
classify-consensus-blast	pipeline	BLAST+ consensus taxonomy classifier
classify-consensus-vsearch	pipeline	VSEARCH-based consensus taxonomy classifier
classify-hybrid-vsearch-sklearn	pipeline	ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier

Artifact Classes¶

Formats¶

This QIIME 2 plugin supports taxonomic classification of features using a variety of methods, including Naive Bayes, vsearch, and BLAST+.

version: 2024.10.0
website: https://github.com/qiime2/q2-feature-classifier
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Bokulich et al., 2018

Actions¶

Name	Type	Short Description
fit-classifier-sklearn	method	Train an almost arbitrary scikit-learn classifier
classify-sklearn	method	Pre-fitted sklearn-based taxonomy classifier
fit-classifier-naive-bayes	method	Train the naive_bayes classifier
extract-reads	method	Extract reads from reference sequences.
find-consensus-annotation	method	Find consensus among multiple annotations.
makeblastdb	method	Make BLAST database.
blast	method	BLAST+ local alignment search.
vsearch-global	method	VSEARCH global alignment search
classify-consensus-blast	pipeline	BLAST+ consensus taxonomy classifier
classify-consensus-vsearch	pipeline	VSEARCH-based consensus taxonomy classifier
classify-hybrid-vsearch-sklearn	pipeline	ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier

Artifact Classes¶

Formats¶

This QIIME 2 plugin supports taxonomic classification of features using a variety of methods, including Naive Bayes, vsearch, and BLAST+.

version: 2024.10.0
website: https://github.com/qiime2/q2-feature-classifier
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Bokulich et al., 2018

Actions¶

Name	Type	Short Description
fit-classifier-sklearn	method	Train an almost arbitrary scikit-learn classifier
classify-sklearn	method	Pre-fitted sklearn-based taxonomy classifier
fit-classifier-naive-bayes	method	Train the naive_bayes classifier
extract-reads	method	Extract reads from reference sequences.
find-consensus-annotation	method	Find consensus among multiple annotations.
makeblastdb	method	Make BLAST database.
blast	method	BLAST+ local alignment search.
vsearch-global	method	VSEARCH global alignment search
classify-consensus-blast	pipeline	BLAST+ consensus taxonomy classifier
classify-consensus-vsearch	pipeline	VSEARCH-based consensus taxonomy classifier
classify-hybrid-vsearch-sklearn	pipeline	ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier

Artifact Classes¶

Formats¶

This QIIME 2 plugin supports taxonomic classification of features using a variety of methods, including Naive Bayes, vsearch, and BLAST+.

version: 2024.10.0
website: https://github.com/qiime2/q2-feature-classifier
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Bokulich et al., 2018

Actions¶

Name	Type	Short Description
fit-classifier-sklearn	method	Train an almost arbitrary scikit-learn classifier
classify-sklearn	method	Pre-fitted sklearn-based taxonomy classifier
fit-classifier-naive-bayes	method	Train the naive_bayes classifier
extract-reads	method	Extract reads from reference sequences.
find-consensus-annotation	method	Find consensus among multiple annotations.
makeblastdb	method	Make BLAST database.
blast	method	BLAST+ local alignment search.
vsearch-global	method	VSEARCH global alignment search
classify-consensus-blast	pipeline	BLAST+ consensus taxonomy classifier
classify-consensus-vsearch	pipeline	VSEARCH-based consensus taxonomy classifier
classify-hybrid-vsearch-sklearn	pipeline	ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier

Artifact Classes¶

Formats¶

This QIIME 2 plugin supports taxonomic classification of features using a variety of methods, including Naive Bayes, vsearch, and BLAST+.

version: 2024.10.0
website: https://github.com/qiime2/q2-feature-classifier
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Bokulich et al., 2018

Actions¶

Name	Type	Short Description
fit-classifier-sklearn	method	Train an almost arbitrary scikit-learn classifier
classify-sklearn	method	Pre-fitted sklearn-based taxonomy classifier
fit-classifier-naive-bayes	method	Train the naive_bayes classifier
extract-reads	method	Extract reads from reference sequences.
find-consensus-annotation	method	Find consensus among multiple annotations.
makeblastdb	method	Make BLAST database.
blast	method	BLAST+ local alignment search.
vsearch-global	method	VSEARCH global alignment search
classify-consensus-blast	pipeline	BLAST+ consensus taxonomy classifier
classify-consensus-vsearch	pipeline	VSEARCH-based consensus taxonomy classifier
classify-hybrid-vsearch-sklearn	pipeline	ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier

Artifact Classes¶

Formats¶

This QIIME 2 plugin supports taxonomic classification of features using a variety of methods, including Naive Bayes, vsearch, and BLAST+.

version: 2024.10.0
website: https://github.com/qiime2/q2-feature-classifier
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Bokulich et al., 2018

Actions¶

Name	Type	Short Description
fit-classifier-sklearn	method	Train an almost arbitrary scikit-learn classifier
classify-sklearn	method	Pre-fitted sklearn-based taxonomy classifier
fit-classifier-naive-bayes	method	Train the naive_bayes classifier
extract-reads	method	Extract reads from reference sequences.
find-consensus-annotation	method	Find consensus among multiple annotations.
makeblastdb	method	Make BLAST database.
blast	method	BLAST+ local alignment search.
vsearch-global	method	VSEARCH global alignment search
classify-consensus-blast	pipeline	BLAST+ consensus taxonomy classifier
classify-consensus-vsearch	pipeline	VSEARCH-based consensus taxonomy classifier
classify-hybrid-vsearch-sklearn	pipeline	ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier

Artifact Classes¶

Formats¶