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.

       --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

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