# pysam

> Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data proces

- Source: https://doutorai.pt/en/components/skills__pysam
- Type: Skills
- Category: Scientific
- Downloads: 9
- Site: Doutor AI (https://doutorai.pt/en) - AI tools for small businesses

An open-source community component, curated and adapted by Doutor AI.

## What it does and how to use it

A **skill** that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

1. Install the skill (command above).
2. In Claude Code, describe what you need - the skill turns on by itself when the context fits.
3. No commands to memorize: you talk in plain language and the skill does the rest.

## Install (Claude Code)

```bash
mkdir -p .claude/skills/pysam && curl -fsSL https://doutorai.pt/data/lib/skills__pysam.md -o .claude/skills/pysam/SKILL.md
```

Paste this command into the terminal, in your project folder, and the component installs automatically.

## Content

```
---
name: pysam
description: "Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines."
---

# Pysam

## Overview

Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant files, and FASTA/FASTQ sequences with a Pythonic interface to htslib. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.

## When to Use This Skill

This skill should be used whe

- 🔒 Full content on the Pro plan (€7.99/month) -
```

## Related components

- [PocketBase API Rules](https://doutorai.pt/en/components/skills__pocketbase-api-rules): API rules and filter expressions for PocketBase access control. Use when setting permissions, writing filter expressions, configuring who ca
- [PocketBase Collections](https://doutorai.pt/en/components/skills__pocketbase-collections): Collection and schema design for PocketBase. Use when creating collections, designing schemas, adding fields, setting up relations, or choos
- [PocketBase Deploy](https://doutorai.pt/en/components/skills__pocketbase-deploy): Production deployment for PocketBase. Use when deploying PocketBase to a server, setting up Docker, configuring systemd, reverse proxy (ngin
- [PocketBase Hooks](https://doutorai.pt/en/components/skills__pocketbase-hooks): Server-side JavaScript hooks for PocketBase (pb_hooks). Use when writing custom routes, event hooks, cron jobs, sending emails, making HTTP 
- [PocketBase Migrations](https://doutorai.pt/en/components/skills__pocketbase-migrations): Schema migrations and versioning for PocketBase. Use when creating migrations, managing schema versions, syncing collections between environ
- [PocketBase SDK](https://doutorai.pt/en/components/skills__pocketbase-sdk): JavaScript SDK usage for PocketBase client applications. Use when calling PocketBase from frontend or Node.js, authenticating users, subscri

## Save hours every week with AI, no hassle

**Doutor AI** gives you 1,859 ready-to-copy AI prompts, by industry and in plain English - plus a complete technical library for those who want to go further. [See plans →](https://doutorai.pt/en/pricing)

---
Content by Doutor AI (https://doutorai.pt/en). When quoting, please cite the source: https://doutorai.pt/en/components/skills__pysam