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Currently, you have to either pull (internet access required) taxa from NCBI post-kraken2, manually pull (also internet-requiring) AND/OR skip kraken2 and use a local reference FASTA file. However, some would want to just use a full Refseq set of FASTA files (many directories/subdirectories) and extract those for the realignment step.
Considerations:
Read the headers of all files is too unwieldy.
Consider supplying a mapping file of accession to file OR extract accession from the filename itself like GCF....fasta
The text was updated successfully, but these errors were encountered:
Description of feature
Currently, you have to either pull (internet access required) taxa from NCBI post-kraken2, manually pull (also internet-requiring) AND/OR skip kraken2 and use a local reference FASTA file. However, some would want to just use a full Refseq set of FASTA files (many directories/subdirectories) and extract those for the realignment step.
Considerations:
Read the headers of all files is too unwieldy.
Consider supplying a mapping file of accession to file OR extract accession from the filename itself like GCF....fasta
The text was updated successfully, but these errors were encountered: