rnalysis.fastq.kallisto_create_index

rnalysis.fastq.kallisto_create_index(transcriptome_fasta: str | Path, kallisto_installation_folder: str | Path | Literal['auto'] = 'auto', kmer_length: PositiveInt = 31, make_unique: bool = False)

builds a kallisto index from a FASTA formatted file of target sequences (transcriptome). The index file will be saved in the same folder as your FASTA file, with the .idx suffix. Be aware that there are pre-built kallisto indices for popular model organisms. These can be downloaded from the kallisto transcriptome indices site.

Parameters:

  • transcriptome_fasta (str or Path) – Path to the FASTA file of your desired transcriptome.

  • kallisto_installation_folder (str, Path, or 'auto' (default='auto')) – Path to the installation folder of kallisto. For example: β€˜C:/Program Files/kallisto’. if installation folder is set to β€˜auto’, RNAlysis will attempt to find it automatically.

  • kmer_length (an odd int between 1 and 31 (default=31)) – k-mer length of the index.

  • make_unique (bool (default=False)) – if True, replace repeated target names with unique names.