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Basic workflow:
Code:
cd tourmaline/02-denoised/dada2-pe # metablast and store as ASN.1 (convertible to any format) blastn \ -query representative_sequences.fasta \ -db $EXTDRIVE/databases/blast/nt/nt \ -negative_gilist $DB/blast/nt/env_metag_unclassified.gi \ -task megablast \ -max_target_seqs 5 \ -max_hsps 1 \ -num_threads 24 \ -outfmt 11 \ -out representative_sequences_vs_nt.asn # convert ASN.1 to XML blast_formatter \ -archive representative_sequences_vs_nt.asn \ -outfmt 5 \ -out representative_sequences_vs_nt.xml # parse XML to TSV (requires BioPython) parse_blast_xml.py \ representative_sequences_vs_nt.xml 1 > \ representative_sequences_vs_nt.tsv # map accessions to taxids (from A to Z), # lookup lineages, and # format as qiime2 taxonomy # RUN: blastn_tsv_to_taxonomy_tsv.ipynb # OUTPUT: representative_sequences_vs_nt_tax.tsv, representative_sequences_taxonomy.tsv # import as qiime2 taxonomy artifact qiime tools import \ --type 'FeatureData[Taxonomy]' \ --input-format TSVTaxonomyFormat \ --input-path representative_sequences_taxonomy.tsv \ --output-path representative_sequences_taxonomy.qza
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Basic workflow:
Code:
The text was updated successfully, but these errors were encountered: