bio-paired-end-fastq
Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-paired-end-fastq --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Paired-End FASTQ **"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. ## Required Import ```python from Bio import SeqIO ``` ## 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` ## Iterate Pairs Together ### Basic Paired Iteration ```python r1_records = SeqIO.parse('reads_R1.fastq', 'fastq') r2_records = SeqIO.parse('reads_R2.fastq', 'fastq') for r1, r2 in zip(r1_records, r2_records): print(f'R1: {r1.id}, R2: {r2.id}')
- Version Compatibility
- Required Import
- Paired File Naming Conventions
- Iterate Pairs Together
- Basic Paired Iteration
- Verify Pair Matching
- Filter Pairs Together
- Filter by Quality (Both Must Pass)
- Filter by Length (Both Must Pass)
- Memory-Efficient Paired Filtering
- Interleave Pairs
- Create Interleaved File
- Interleave with Modified IDs
- Deinterleave
What does the bio-paired-end-fastq skill do?
Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-paired-end-fastq --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.