bio-paired-end-fastq

Paired File Naming Conventions

Common patterns for paired files:

• sample_R1.fastq / sample_R2.fastq
• sample_1.fastq / sample_2.fastq
• sample_R1_001.fastq / sample_R2_001.fastq

Memory-Efficient Paired Filtering

Goal: Quality-filter paired reads while maintaining R1/R2 synchronization without loading all reads into memory.

Approach: Stream both files in lockstep with zip, evaluate both mates, and write only pairs where both pass.

Reference (BioPython 1.83+):

Create Interleaved File

Goal: Merge separate R1/R2 files into a single interleaved file (R1, R2, R1, R2, ...).

Approach: Zip both iterators together and yield alternating records through a generator.

Reference (BioPython 1.83+):