salmon index

Reference Code backup Executable files

Create a salmon index

Category

Mapping

Usage

salmon index [options] -t transcript.fa -i index_name

Manual

Required arguments

  • -t, --transcripts string: Transcript fasta file
  • -i, --index string: Salmon index

Options

  • -v, --version: Print version string
  • -h, --help: Produce help message
  • -k, --kmerLen int (=31): The size of k-mers that should be used for the quasi 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 int (=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 int (=-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 string: 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 string: Treat these sequence IDs from the reference as the decoys that may have sequence homologous to some known transcript. For example, in the case of the genome, provide a list of chromosome names --- one per line.
  • -n, --no-clip: Don't clip poly-A tails from the ends of target sequences.
  • --type string (=puff): The type of index to build; the only option is "puff" in this version of salmon.

File formats this tool works with
FASTA

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