.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.3.
.TH SALMON_INDEX "1" "June 2021" "salmon --no-version-check index 1.4.0+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\-\-features\fR
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.
.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 during indexing.
.TP
\fB\-\-keepFixedFasta\fR
Retain the fixed fasta file (without short
transcripts and duplicates, clipped, etc.)
generated during indexing
.TP
\fB\-f\fR [ \fB\-\-filterSize\fR ] 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 \fB\-1\fR
means that the filter size will be
automatically set based on the number of
distinct k\-mers in the input, as estimated by
nthll.
.TP
\fB\-\-tmpdir\fR 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.
.TP
\fB\-\-sparse\fR
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
.TP
\fB\-d\fR [ \fB\-\-decoys\fR ] 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
\fB\-\-\-\fR one per line
.TP
\fB\-\-type\fR arg (=puff)
The type of index to build; the only option is
"puff" in this version of salmon.