Genome preparation

Bismark needs to prepare the bisulfite index for the genome.

• In the current pipeline, user can provide the genome.fasta and the pipeline can index it.

• Optinally, user can provide the index files directly, and the pipeline will use it without indexing the genome again.

Key Options

• --verbose: Prints detailed output during the indexing process.

• --parallel <threads>: Uses multiple threads to speed up genome preparation.

• --bowtie2: Specifies that Bowtie2 will be used for alignment (default option in most versions).

• --path_to_bowtie <path>: Specifies the path to the Bowtie installation if not in your PATH.

Example with Options:

bismark_genome_preparation --bowtie2 --parallel 4 <genome.fasta>

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4. Output

After successful completion, Bismark generates a bisulfite-converted genome in two orientations (C->T and G->A) along with the Bowtie/Bowtie2 indices.

Output directory structure:

your_path_to_reference/
    Bisulfite_Genome/
        CT_conversion/
        GA_conversion/
        genome.1.bt2
        genome.2.bt2
        ...