Provided by: salmon_0.7.2+ds1-3_amd64 
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.
-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; options are "fmd" and "quasi" "quasi" is recommended, and "fmd" may be
removed in the future
-s [ --sasamp ] arg (=1)
The interval at which the suffix array should be sampled. Smaller values are faster, but produce a
larger index. The default should be OK, unless your transcriptome is huge. This value should be a
power of 2.