index command

The index command has two forms of input; either it will take a reference genome FASTA and GTF as input, from which it can build a spliced+intronic (splici) reference or a spliced+unspliced (spliceu) reference using roers (which is used as a library directly from simpleaf, and so need not be installed independently), or it will take a single reference sequence file (i.e. FASTA file) as input (direct-ref mode).

In expanded reference mode, after the expanded reference is constructed, the resulting reference will be indexed with piscem build or salmon index command (depending on the mapper you choose to use), and a copy of the 3-column transcript-to-gene file will be placed in the index directory for subsequent use. The output directory will contain both a ref and index subdirectoy, with the first containing the splici reference that was extracted from the provided genome and GTF, and the latter containing the index built on this reference.

In direct-ref mode, the provided fasta file (passed in with --refseq) will be provided to piscem build or salmon index directly. The output diretory will contain an index subdirectory that contains the index built on this reference.

The relevant options (which you can obtain by running simpleaf index -h) are:

build the (expanded) reference index

Usage: simpleaf index [OPTIONS] --output <OUTPUT> <--fasta <FASTA>|--ref-seq <REF_SEQ>>

Options:
  -o, --output <OUTPUT>            path to output directory (will be created if it doesn't exist)
  -t, --threads <THREADS>          number of threads to use when running [default: 16]
  -k, --kmer-length <KMER_LENGTH>  the value of k to be used to construct the index [default: 31]
      --keep-duplicates            keep duplicated identical sequences when constructing the index
  -p, --sparse                     if this flag is passed, build the sparse rather than dense index for mapping
  -h, --help                       Print help information
  -V, --version                    Print version information

Expanded Reference Options:
      --ref-type <REF_TYPE>    specify whether an expanded reference, spliced+intronic (or splici) or spliced+unspliced (or spliceu), should be built [default: spliced+intronic]
  -f, --fasta <FASTA>          reference genome to be used for the expanded reference construction
  -g, --gtf <GTF>              reference GTF file to be used for the expanded reference construction
  -r, --rlen <RLEN>            the target read length the splici index will be built for
      --dedup                  deduplicate identical sequences in roers when building an expanded reference  reference
      --spliced <SPLICED>      path to FASTA file with extra spliced sequence to add to the index
      --unspliced <UNSPLICED>  path to FASTA file with extra unspliced sequence to add to the index

Direct Reference Options:
      --ref-seq <REF_SEQ>  target sequences (provide target sequences directly; avoid expanded reference construction)

Piscem Index Options:
      --use-piscem                           use piscem instead of salmon for indexing and mapping
  -m, --minimizer-length <MINIMIZER_LENGTH>  the value of m to be used to construct the piscem index (must be < k) [default: 19]