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Build Salmon Index

Source: R/salmon_utils.R
salmon_index.Rd

Create a Salmon index from a reference transcriptome FASTA file.

Usage

salmon_index(
  fasta_path,
  index_path = "salmon_index",
  kmer_len = 31,
  num_threads = 2,
  env_name = "salmon-env",
  is_gencode = FALSE,
  decoy_fasta = NULL,
  clip_poly_a = TRUE
)

Arguments

fasta_path

Path to the reference transcriptome FASTA file.

index_path

Directory path to save the Salmon index (default is "salmon_index").

kmer_len

K-mer length for the index (default is 31).

num_threads

Number of threads to use (default is 2).

env_name

Name of the conda environment with Salmon installed (default is "salmon-env").

is_gencode

Logical indicating if the FASTA is from GENCODE (default is FALSE); the transcript names are then truncated at the first | so that they match the annotation.

decoy_fasta

Optional path to a FASTA file containing decoy sequences (default is NULL).

clip_poly_a

Logical indicating whether to clip poly-A tails (default is TRUE).

Value

processx style output list.

Details

The index must be built with the same Salmon major version used for salmon_quant(): Salmon 2 (the Rust rewrite) cannot read indices built by Salmon 1.x and rejects them with an error. Rebuild the index after upgrading.