rnalysis.fastq.bowtie2_create_index

rnalysis.fastq.bowtie2_create_index(genome_fastas: List[str | Path], output_folder: str | Path, index_name: str | Literal['auto'] = 'auto', bowtie2_installation_folder: str | Path | Literal['auto'] = 'auto', random_seed: NonNegativeInt | None = None, threads: PositiveInt = 1)

builds a bowtie index from FASTA formatted files of target sequences (genome). The index files will be saved in the same folder as your first FASTA file, with the .bt2 suffix. Be aware that there are pre-built bowtie2 indices for popular model organisms. These can be downloaded from the bowtie2 website (from menu on the right).

Parameters:

  • genome_fastas (list of str or Path) – Path to the FASTA file/files which contain reference sequences to be aligned to.

  • output_folder (str or Path) – Path to the folder in which the bowtie2 index files will be saved.

  • index_name (str or 'auto' (default='auto')) – The basename of the index files. bowtie2 will create files named index_name.1.bt2, index_name.2.bt2, index_name.3.bt2, index_name.4.bt2, index_name.rev.1.bt2, and index_name.rev.2.bt2. if index_name=’auto’, the index name used will be the stem of the first supplied genome FASTA file (for example: if the first genome FASTA file is ‘path/to/genome.fa.gz’, the index name will be ‘genome’).

  • bowtie2_installation_folder – Path to the installation folder of bowtie2. For example:

‘C:/Program Files/bowtie2-2.5.1’. if installation folder is set to ‘auto’, RNAlysis will attempt to find it automatically. :type bowtie2_installation_folder: str, Path, or ‘auto’ (default=’auto’) :param random_seed: if specified, determines the seed for pseudo-random number generator. :type random_seed: int >=0 or None (default=None) :param threads: number of threads to run bowtie2-build on. More threads will generally make index building faster. :type threads: int > 0 (default=1)