.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SALMON_INDEX "1" "January 2019" "salmon_index 0.12.0+ds1" "User Commands"
.SH NAME
salmon_index \- highly-accurate, transcript-level quantification estimates from RNA-seq data 
.SH DESCRIPTION
Index
==========
Creates a salmon index.
.SS "Command Line Options:"
.TP
\fB\-v\fR [ \fB\-\-version\fR ]
print version string
.TP
\fB\-h\fR [ \fB\-\-help\fR ]
produce help message
.TP
\fB\-t\fR [ \fB\-\-transcripts\fR ] arg
Transcript fasta file.
.TP
\fB\-k\fR [ \fB\-\-kmerLen\fR ] arg (=31) The size of k\-mers that should be used for the
quasi index.
.TP
\fB\-i\fR [ \fB\-\-index\fR ] arg
salmon index.
.TP
\fB\-\-gencode\fR
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.
.TP
\fB\-\-keepDuplicates\fR
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.
.TP
\fB\-p\fR [ \fB\-\-threads\fR ] arg (=2)
Number of threads to use (only used for computing
bias features)
.TP
\fB\-\-perfectHash\fR
[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
.TP
\fB\-\-type\fR arg (=quasi)
The type of index to build; the only option is
"quasi" in this version of salmon.