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pysam-developers / pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://pysam.readthedocs.io/en/latest/
MIT License
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Long Pac-Bio reads #1090

Open HRtech-lab opened 2 years ago

HRtech-lab commented 2 years ago

Does pysam work with long Pac-Bio reads and ONT read?

AndreasHeger commented 2 years ago

Yes, it should. I have used it with ONT reads in the past.

pysam relies on all of its functionality on htslib, and htslib is, AFAIK, able to handle long reads.

HRtech-lab commented 2 years ago

Hello @AndreasHeger I am trying on Pac-bio reads. I will update you if it works properly on Pac-bio as desired. Pysam is a great htslib wrapper and its actually fast. I would like to thank you for making such a wonderful library in python.

HRtech-lab commented 2 years ago

Hello @AndreasHeger Just to let you know I worked with Pacbio reads and Pysam works fine with it.