NAME

       salmon_index  -  highly-accurate,  transcript-level  quantification estimates from RNA-seq
       data

DESCRIPTION

       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.

       --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 (only used for computing bias features)

       --perfectHash
              [quasi  index  only] Build the index using a perfect hash rather than a dense hash.
              This will require less memory (especially during  quantification),  but  will  take
              longer to construct

       --type arg (=quasi)
              The type of index to build; the only option is "quasi" in this version of salmon.