Bedutils

Bedutils manipulates and manages next-generation sequencing (NGS) data, providing operations for FASTQ, BED, and BAM formats to handle sequence reads, genomic intervals, and aligned sequences.

Key Features:

• Modular Design: Modular architecture enables integration of specific components into existing analysis pipelines.
• FASTQ support: Handles raw sequencing reads stored in FASTQ format.
• BED support: Manipulates genomic intervals and annotations in BED format.
• BAM support: Processes aligned sequence data in BAM format and facilitates downstream analyses such as variant calling and expression profiling.

Scientific Applications:

• Data Preprocessing: Streamlines initial handling of raw sequencing data.
• Annotation and Analysis: Facilitates genomic interval manipulations and annotations relevant to gene function and regulation studies.
• Alignment Processing: Manages aligned sequence data to support differential expression analyses and variant discovery.

Methodology:

Implemented in Python 2.6 or higher and leveraging virtualenv for dependency and environment management.