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Sean Bresnahan authored Jan 30, 2023
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# metacleaner
## Automated curation of barcode sequence databases for metabarcoding and metagenomics

Reference sequence databases generated by tools like [MetaCurator](https://github.com/RTRichar/MetaCurator) sometimes contain falsely labelled accessions (e.g., see: https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13314). In particular, we found that pollen metabarcoding experiments using plant ITS1 and ITS2 region databases generated by MetaCurator would yield many Sanger reads corresponding to random sequences in fungi, or to ITS1/ITS2 sequences in plants of the wrong genera or multiple genera at the same % identity and query coverage.
DNA barcode reference databases generated by tools like [MetaCurator](https://github.com/RTRichar/MetaCurator) - which operate on sequences retrieved from NCBI - sometimes contain falsely labelled accessions (e.g., see: https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13314). In particular, we found that pollen metabarcoding experiments using plant ITS1 and ITS2 region databases would yield many Sanger reads corresponding to random sequences in fungi, or to ITS1/ITS2 sequences in plants of the wrong genera or multiple genera at the same % identity and query coverage.

metacleaner takes as input a `.fasta` file generated by tools like MetaCurator, and searches for hits against "good" and "bad" sequence databases to filter undesired accessions before downstream use.
metacleaner takes as input a `.fasta` file and searches for hits against "good" and "bad" sequence databases to filter undesired accessions before downstream use.

### Workflow:
1) Query sequences are searched for hits against known undesired sequences using blastn; query sequences with hits above user-defined thresholds for percentage identity (pident) and query coverage (qcovs) are flagged as mislabeled.
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