{"id":12,"date":"2024-04-04T08:51:36","date_gmt":"2024-04-04T05:51:36","guid":{"rendered":"https:\/\/sisu.ut.ee\/eukaryome\/reference-based-chimera-detection\/"},"modified":"2024-06-25T10:54:15","modified_gmt":"2024-06-25T07:54:15","slug":"reference-based-chimera-detection","status":"publish","type":"page","link":"https:\/\/sisu.ut.ee\/eukaryome\/reference-based-chimera-detection\/","title":{"rendered":"Reference-based chimera detection"},"content":{"rendered":"

\n1. UCHIME reference-based chimera detection<\/strong><\/span><\/span><\/p>\n

Using the EUKARYOME database for the reference-based chimera filtering process in USEARCH or VSEARCH (\u2013uchime_ref):<\/span><\/span><\/p>\n

\u00a0<\/span><\/p>\n

vsearch --uchime_ref your_sequences.fasta \n--db General_EUK_ITS_v1.8.fasta \n--nonchimeras nonchimeras.fasta\n<\/pre>\n
\n<\/p>
2. QIIME 2 reference-based chimera detection<\/strong><\/span><\/span><\/p>\n
\nInitially, you should change the format to the \u201c.qza\u201d format and import the files into QIIME 2:<\/span><\/p>\n
 \u00a0<\/span><\/p>\n
Importing the taxonomy file:<\/strong><\/span><\/p>\n
\nqiime tools import --type 'FeatureData[Taxonomy]' --input-path QIIME2_EUK_SSU_v1.8.tsv --output-path eukaryome_tax.qza\n<\/code><\/pre>\n
Importing the sequence file:<\/strong><\/span><\/p>\n
\nqiime tools import --input-path QIIME2_EUK_SSU_v1.8.fasta --output-path eukaryome_seq.qza --type 'FeatureData[Sequence]'<\/code><\/pre>\n
\nQIIME 2 uses the VSEARCH plugin for reference-based chimera detection. Here\u2019s how you can use it:<\/span>\n<\/p>\n
qiime vsearch uchime-ref \n\n--i-table table.qza \n\n--i-sequences your-seqs.qza \n\n--i-reference-sequences eukaryome_seq.qza \n\n--o-nonchimeras  nonchimeras.qza\n<\/pre>\n
\nIt takes as input:<\/span><\/p>\n
    \n
  • \n
    table.qza: The feature table was obtained from the sequence quality control step.<\/span><\/p>\n<\/li>\n
  • \n
    your-seqs.qza: The representative sequences obtained from the sequence quality control step.<\/span><\/p>\n<\/li>\n
  • \n
    eukaryome_seq.qza: A reference database of chimeric sequences<\/span><\/p>\n<\/li>\n
  • \n
    nonchimeras.qza: The output file where non-chimeric sequences will be stored<\/span><\/p>\n<\/li>\n<\/ul>\n
     \u00a0<\/span><\/p>\n
    3. Mothur reference-based chimera detection<\/strong><\/span><\/span><\/p>\n
    mothur provides the chimera.uchime command for reference-based chimera detection:<\/span><\/p>\n
    mothur \"#chimera.uchime(fasta=your_sequences.fasta, reference=mothur_EUK_SSU.v1.8.fasta)\"\n<\/pre>\n
    \n<\/p>
    \n<\/p>","protected":false},"excerpt":{"rendered":"
    1. UCHIME reference-based chimera detection Using the EUKARYOME database for the reference-based chimera filtering process in USEARCH or VSEARCH (\u2013uchime_ref): \u00a0 vsearch –uchime_ref your_sequences.fasta –db General_EUK_ITS_v1.8.fasta –nonchimeras nonchimeras.fasta 2. QIIME 2 reference-based chimera detection Initially, you should change the format …<\/p>\n","protected":false},"author":163,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"class_list":["post-12","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/12","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/users\/163"}],"replies":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/comments?post=12"}],"version-history":[{"count":2,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/12\/revisions"}],"predecessor-version":[{"id":321,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/12\/revisions\/321"}],"wp:attachment":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/media?parent=12"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}