```bash
salmon index -h
```

Version Info: This is the most recent version of salmon.

Index
==========
Creates a salmon index.

Command Line Options:
  -v [ --version ]              print version string
  -h [ --help ]                 produce help message
  -t [ --transcripts ] arg      Transcript fasta file.
  -k [ --kmerLen ] arg (=31)    The size of k-mers that should be used for the 
                                quasi index.
  -i [ --index ] arg            salmon index.
  --gencode                     This flag will expect the input transcript 
                                fasta to be in GENCODE format, and will split 
                                the transcript name at the first '|' character.
                                These reduced names will be used in the output 
                                and when looking for these transcripts in a 
                                gene to transcript GTF.
  --features                    This flag will expect the input reference to be
                                in the tsv file format, and will split the 
                                feature name at the first 'tab' character. 
                                These reduced names will be used in the output 
                                and when looking for the sequence of the 
                                features.GTF.
  --keepDuplicates              This flag will disable the default indexing 
                                behavior of discarding sequence-identical 
                                duplicate transcripts.  If this flag is passed,
                                then duplicate transcripts that appear in the 
                                input will be retained and quantified 
                                separately.
  -p [ --threads ] arg (=2)     Number of threads to use during indexing.
  --keepFixedFasta              Retain the fixed fasta file (without short 
                                transcripts and duplicates, clipped, etc.) 
                                generated during indexing
  -f [ --filterSize ] arg (=-1) The size of the Bloom filter that will be used 
                                by TwoPaCo during indexing. The filter will be 
                                of size 2^{filterSize}. The default value of -1
                                means that the filter size will be 
                                automatically set based on the number of 
                                distinct k-mers in the input, as estimated by 
                                nthll.
  --tmpdir arg                  The directory location that will be used for 
                                TwoPaCo temporary files; it will be created if 
                                need be and be removed prior to indexing 
                                completion. The default value will cause a 
                                (temporary) subdirectory of the salmon index 
                                directory to be used for this purpose.
  --sparse                      Build the index using a sparse sampling of 
                                k-mer positions This will require less memory 
                                (especially during quantification), but will 
                                take longer to construct and can slow down 
                                mapping / alignment
  -d [ --decoys ] arg           Treat these sequences ids from the reference as
                                the decoys that may have sequence homologous to
                                some known transcript. for example in case of 
                                the genome, provide a list of chromosome name 
                                --- one per line
  -n [ --no-clip ]              Don't clip poly-A tails from the ends of target
                                sequences
  --type arg (=puff)            The type of index to build; the only option is 
                                "puff" in this version of salmon.
