Kallisto is used for estimating transcript abundance from rna-seq data without conventional alignment. I am unsure about the usage of Kallisto.

I basically have 4 files to start with. I have paired-end rna-seq data with 2 fastq files. And I have a reference genome and transcriptome fasta files from Ensembl. The first step is building an index shown in the help as such:

kallisto index -i transcripts.idx transcripts.fasta.gz

What is transcripts.idx and transcripts.fasta.gz? Where do they come from? Do I need to use the reference genome or transcriptome here?

And then the quantification as such:

kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz

The transcripts.idx here again? Can someone explain how do I go about with this workflow given my 4 files (f.fq, r.fq, refgenome.fa, reftranscriptome.fa)? Thanks.