baitUtils

Overview

baitUtils is a comprehensive toolkit for the analysis and visualization of bait sequences used in in-solution hybridization. It provides tools for generating bait quality statistics and visualizations.

Installation

Prerequisites

• Conda: Please ensure you have conda installed to manage dependencies.
• Install the required packages and dependencies with:

conda create -n baitutils_env numpy pandas matplotlib-base seaborn scikit-learn biopython viennarna pblat
conda activate baitutils_env

Clone the Repository

git clone https://github.com/FOI-Bioinformatics/baitUtils.git
cd baitUtils
pip install .

Usage

General Structure

baitUtils offers two main functionalities: stats and plot, both accessible as subcommands of the primary script.

baitUtils [command] [options]

Commands

• stats: Calculate quality statistics of bait sequences.
• plot: Generate plots based on bait sequence statistics.

Commands and Options

baitUtils stats

Calculates statistics on bait sequences and filters them based on user-defined criteria.

Example Usage

baitUtils stats -i probes.fasta.gz -o results --length 120 --mingc 40 --maxgc 60 --filter

Options

• -i, --input: Path to the input FASTA or FASTA.GZ file.
• -o, --outdir: Output directory for results.
• --length: Requested bait length (default is 120).
• --mingc: Minimum GC content percentage.
• --maxgc: Maximum GC content percentage.
• --filter: Save filtered FASTA output.

baitUtils plot

Generates plots based on the bait sequence statistics file.

Example Usage

baitUtils plot -i results/filtered-params.txt -o plots --columns GC% Tm MFE --plot_type histogram boxplot scatterplot

Options

• -i, --input: Path to the parameters file.
• -o, --outdir: Output directory for plots.
• --columns: List of columns to include in plots.
• --plot_type: Types of plots to generate.
• --color: Column to use for coloring plots.

baitUtils map

Maps bait sequences against a reference genome using pblat and filters mappings based on identity percentage.

Example Usage

baitUtils map -i baits.fa -q genome.fa -o mapping_results --outdir mappings --threads 4 --minIdentity 90 --filterIdentity 95 --fasta-output both

Options

• -i, --input: Path to the input baits FASTA file.
• -q, --query: Path to the reference genome FASTA file to map against.
• -o, --outprefix: Prefix for the output files (default is out).
• -Z, --outdir: Output directory path (default is .).
• --mapper: Mapping tool to use (pblat is currently supported).
• -X, --threads: Number of threads to use for mapping (default is 1).
• --minMatch: Minimum number of tile matches (default is 2 for nucleotide sequences).
• --minScore: Minimum score for alignments (default is 30).
• --minIdentity: Minimum sequence identity percentage for mappings (default is 90).
• --filterIdentity: Filter mappings with identity percentage less than this value; must be ≥ minIdentity (default is 90).
• --fasta-output: Choose which probes to include in the FASTA output file: mapped, unmapped, both, or none (default is mapped).
• -l, --log: Enable detailed logging for execution insights.

Examples

Stats Example

To calculate and filter baits based on length, GC content, and other quality metrics:

baitUtils stats -i probes.fasta.gz -o stats_output --length 120 --mingc 40 --maxgc 60 --filter

Plot Example

To generate histograms, boxplots, and scatterplots for GC content and melting temperature:

baitUtils plot -i stats_output/filtered-params.txt -o plots_output --columns GC% Tm --plot_type histogram scatterplot --color Kept

Map Example

To map baits against a reference genome and output both mapped and unmapped probes:

baitUtils map -i baits.fa -q genome.fa -o mapping_results --outdir mappings --threads 4 --minIdentity 90 --filterIdentity 95 --fasta-output both

License

MIT License. See LICENSE file for details.