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README.md

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 # metacleaner
 ## Automated curation of barcode sequence databases for metabarcoding and metagenomics
 
-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. 
+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 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. You can read a detailed report of this problem using an example dataset on [my research website](https://seantbresnahan.com/metacleaner/).
 
 metacleaner takes as input a `.fasta` file and searches for hits against "good" and "bad" sequence databases to filter undesired accessions before downstream use.