What genomic file formats does Pysam support?

Pysam supports a wide range of formats including SAM, BAM, and CRAM for sequencing alignments; VCF and BCF for genetic variants; and FASTA and FASTQ for nucleotide sequences.

Does Pysam use 0-based or 1-based coordinates?

Pysam follows the Python convention of 0-based, half-open coordinates. However, region strings used in the fetch() method follow the 1-based samtools convention.

Are index files required for Pysam operations?

Yes, random access to specific genomic regions requires corresponding index files, such as .bai for BAM, .fai for FASTA, and .tbi for compressed VCF files.

Can I run samtools commands through Pysam?

Absolutely. Pysam provides direct access to samtools and bcftools commands via the pysam.samtools and pysam.bcftools modules, allowing you to sort, index, and view files within Python.

Pysam Genomic Toolkit

Name: Pysam Genomic Toolkit
Author: Activer007

byActiver007

데이터 과학 및 ML

Manipulates genomic datasets including SAM, BAM, CRAM, and VCF files through a Pythonic interface to htslib.

소개

Pysam is a comprehensive Python library designed for processing high-throughput sequencing data. It provides a robust interface for reading, writing, and querying various genomic file formats such as alignments (BAM/CRAM), variants (VCF/BCF), and sequences (FASTA/FASTQ). By wrapping the htslib C-API, Pysam allows bioinformaticians and researchers to perform complex tasks like region-specific fetching, pileup analysis for coverage, and integration with samtools and bcftools directly within Python workflows, making it an essential tool for building scalable NGS data processing pipelines.

주요 기능

Efficient random access to FASTA and FASTQ sequences
Advanced pileup analysis for calculating genomic coverage
Full support for SAM, BAM, and CRAM alignment files
0 GitHub stars
Native integration with samtools and bcftools commands
Manipulation and analysis of VCF and BCF variant files

사용 사례

Building Next-Generation Sequencing (NGS) analysis pipelines
Filtering and annotating genetic variants from VCF files
Calculating read depth and genomic coverage for quality control

소개

주요 기능

Efficient random access to FASTA and FASTQ sequences
Advanced pileup analysis for calculating genomic coverage
Full support for SAM, BAM, and CRAM alignment files
0 GitHub stars
Native integration with samtools and bcftools commands
Manipulation and analysis of VCF and BCF variant files

사용 사례

Building Next-Generation Sequencing (NGS) analysis pipelines
Filtering and annotating genetic variants from VCF files
Calculating read depth and genomic coverage for quality control