biobloom
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Create Bloom filters for a given reference and then use it to categorize sequences
Hi, I want to check if there is any viral sequence in my human fastq. I run the BBT according to "Integrated Genomic Characterization of Papillary Thyroid Carcinoma" said. The...
When the minimum FPR is too low for the length of a read + the false postive rate of the bf, the program aborts. Somewhat related to issue #51 ....
Adding average score of classified reads could help in determining if read quality is lower than expected or high rates of divergance may be occuring.
There has been a feature request for spaced seeds to be used in normal BF. Caveats: If multiple spaced seed are used, we can expect memory to increase accordingly to...
Options for minimum match length and expected read size for a would set the occupancy of the filter but would be superceed by a minimum global occupancy if the parameter...
Update biobloomcategorizer, biobloommimaker, and biobloommaker to use producer consumer i/o for faster I/O when multiple threads are used
Would add dependency on ntcard, however would make filter creation more consistent on differnt types of input into biobloommaker.
Prevent or handle properly cases where the same fasta header is seen when using the miBF.