```
kallisto quant
```

kallisto 0.50.1
Computes equivalence classes for reads and quantifies abundances

Usage: kallisto quant [arguments] FASTQ-files

Required arguments:
-i, --index=STRING            Filename for the kallisto index to be used for
                              quantification
-o, --output-dir=STRING       Directory to write output to

Optional arguments:
-b, --bootstrap-samples=INT   Number of bootstrap samples (default: 0)
    --seed=INT                Seed for the bootstrap sampling (default: 42)
    --plaintext               Output plaintext instead of HDF5
    --single                  Quantify single-end reads
    --single-overhang         Include reads where unobserved rest of fragment is
                              predicted to lie outside a transcript
    --fr-stranded             Strand specific reads, first read forward
    --rf-stranded             Strand specific reads, first read reverse
-l, --fragment-length=DOUBLE  Estimated average fragment length
-s, --sd=DOUBLE               Estimated standard deviation of fragment length
                              (default: -l, -s values are estimated from paired
                               end data, but are required when using --single)
-p, --priors                  Priors for the EM algorithm, either as raw counts or as
                              probabilities. Pseudocounts are added to raw reads to
                              prevent zero valued priors. Supplied in the same order
                              as the transcripts in the transcriptome
-t, --threads=INT             Number of threads to use (default: 1)
    --verbose                 Print out progress information every 1M proccessed reads