rescript¶
| Description |
Reference sequence annotation and curation pipeline. |
|---|---|
| Version | 2024.10.0 |
| Website | https://github.com/nbokulich/RESCRIPt |
| Support |
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org |
| q2cli Invocation | qiime rescript
|
| Artifact API Import | from qiime2.plugins import rescript
|
| Citations |
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Pipelines¶
- evaluate-classifications: Interactively evaluate taxonomic classification accuracy.
- evaluate-cross-validate: Evaluate DNA sequence reference database via cross-validated taxonomic classification.
- evaluate-fit-classifier: Evaluate and train naive Bayes classifier on reference sequences.
- evaluate-taxonomy: Compute summary statistics on taxonomy artifact(s).
- get-silva-data: Download, parse, and import SILVA database.
- trim-alignment: Trim alignment based on provided primers or specific positions.
Methods¶
- cull-seqs: Removes sequences that contain at least the specified number of degenerate bases and/or homopolymers of a given length.
- degap-seqs: Remove gaps from DNA sequence alignments.
- dereplicate: Dereplicate features with matching sequences and taxonomies.
- edit-taxonomy: Edit taxonomy strings with find and replace terms.
- extract-seq-segments: Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined ‘perc-identity’ value.
- filter-seqs-length: Filter sequences by length.
- filter-seqs-length-by-taxon: Filter sequences by length and taxonomic group.
- filter-taxa: Filter taxonomy by list of IDs or search criteria.
- get-bv-brc-genome-features: Fetch genome features from BV-BRC.
- get-bv-brc-genomes: Get genome sequences from the BV-BRC database.
- get-bv-brc-metadata: Fetch BV-BCR metadata.
- get-gtdb-data: Download, parse, and import SSU GTDB reference data.
- get-ncbi-data: Download, parse, and import NCBI sequences and taxonomies
- get-ncbi-data-protein: Download, parse, and import NCBI protein sequences and taxonomies
- get-ncbi-genomes: Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.
- get-unite-data: Download and import UNITE reference data.
- merge-taxa: Compare taxonomies and select the longest, highest scoring, or find the least common ancestor.
- orient-seqs: Orient input sequences by comparison against reference.
- parse-silva-taxonomy: Generates a SILVA fixed-rank taxonomy.
- reverse-transcribe: Reverse transcribe RNA to DNA sequences.
- subsample-fasta: Subsample an indicated number of sequences from a FASTA file.