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bio-paired-end-fastq

Maintainer FreedomIntelligence · Last updated April 1, 2026

Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.

OpenClawNanoClawAnalysisReproductionbio-paired-end-fastq🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qchandle

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-paired-end-fastq

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: SeqIO.parse() with zip() iteration (BioPython).
Work with my paired-end FASTQ files" → Iterate R1/R2 pairs in sync, filter both mates together, interleave/deinterleave files, and auto-detect paired file naming. Python: SeqIO.parse() with zip() iteration (BioPython).
Handle paired-end sequencing data (R1/R2 files) using Biopython.

Source Doc

Excerpt From SKILL.md

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+):

Use cases

Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

read-sequences - Parse individual FASTQ files
fastq-quality - Quality filtering before paired processing
filter-sequences - Additional filtering criteria
compressed-files - Handle gzipped paired files
alignment-files - After filtering, align paired reads with bwa mem; proper pairs in BAM