Is it possible to use .fai index in BWA, bowtie, bowtie2 or minimap2? Or.. maybe someone used a classes which allow me to read indexes from these tools in scala programs? I was finding in htsjdk/samtools package, but there is only FastaSequenceIndex (fai)
No, it is not possible to use fai index with bwa or bowtie. The fai index is just a simple text file with information that allows fast retrieval of fasta segments - see Can You Please Tell Me Where I Find Information About .Fai File Format? for a discussion. The bwa and bowtie indices are different implementations of a FM-index, which is "an opportunistic data structure as it allows compression of the input text while still permitting fast substring queries".
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