boquila

Tool for generating synthetic next-generation sequencing reads with same nucleotide distribution as model reads.

Usage

boquila 0.6.1

Generate NGS reads with same nucleotide distribution as input file
Generated reads will be written to stdout
By default input and output format is FASTQ

USAGE:
    boquila [FLAGS] [OPTIONS] <src>

ARGS:
    <src>    Model file

FLAGS:
        --fasta         Change input and output format to FASTA
        --setQual       Use given Quality score with parameter 'qual' for all simulated reads.
    -h, --help          Print help information
        --inseqFasta    Change the input sequencing format to FASTA
    -V, --version       Print version information

OPTIONS:
        --bed <FILE>        File name in which the simulated reads will be saved in BED format
        --inseq <FILE>      Input sequencing reads to be used instead of reference genome
        --kmer <INT>        Kmer size to be used while calculating frequency [default: 1]
        --ref <FILE>        Reference FASTA
        --regions <FILE>    RON formatted file containing genomic regions that generated reads will
                            be selected from
        --seed <INT>        Random number seed. If not provided system's default source of entropy
                            will be used instead.
        --sens <INT>        Sensitivity of selected reads.
                            If some positions are predominated by specific nucleotides, increasing
                            this value can make simulated reads more similar to input reads.
                            However runtime will also increase linearly.
                            [possible values: 10-100] [default: 20]
        --qual <QUAL>       Quality score to be applied to to each position for all reads.
                            'setQual' flag should be present in order it to work
                            Has no effect if input reads are not in FASTQ format. [default: I]

Generated reads will be written to stdout in FASTA or FASTQ format.

If --bed option is provided, generated reads also will be written to given file in BED6 format.

Sample regions file for Homo sapiens (human) genome assembly GRCh38 (hg38) is provided as GRCh38.ron

If Input Sequencing reads will be used for simulation, they should be provided with --inseq argument, instead of using --ref and --regions.

Examples

More detailed example can be found in the examples directory

Simple usage

boquila input_reads.fq --ref ref_genome.fa --regions GRCh38.ron > out.fq

Using seed for RNG

boquila input_reads.fq --ref ref_genome.fa --regions GRCh38.ron --seed 7 > out.fq

Using reads that are in FASTA format

boquila input_reads.fa --fasta --ref ref_genome.fa --regions GRCh38.ron > out.fa

Saving output in BED format

boquila input_reads.fq --ref ref_genome.fa --regions GRCh38.ron --bed out.bed > out.fq

Using Input Sequencing instead of reference genome

boquila input_reads.fq --inseq inputseq_reads.fq > out.fq

Using Input Sequencing reads which are in FASTA format

boquila input_reads.fq --inseqFasta --inseq inputseq_reads.fa > out.fq

Installation

1. boquila is available via bioconda and can be easily installed via

conda install boquila -c bioconda

Or via Rust toolchain

Next two methods require Cargo the Rust package manager, which should be installed automatically while installing Rust

boquila is written in Rust, so you’ll need to grab a Rust installation in order to install or compile it.

The current minimum Rust version is 1.55.0

2. Installing with cargo

Cargo will build and install the binary, by default to $HOME/.cargo/bin/

$ cargo install --branch main --git https://github.com/CompGenomeLab/boquila.git boquila

3. Building from source

For convenience, you can copy the executable ./target/release/boquila to some directory in your PATH.

- Clone the repository
    ```bash
    git clone https://github.com/CompGenomeLab/boquila.git
    ```
- Then build with `cargo`
    ```bash
    cd boquila
    cargo build --release
    ./target/release/boquila --version
    0.6.1
    ```