April 19, 2018

BISTRO - Marcus Sherman

4:00 PM
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2036 Palmer Commons

BISTRO is restricted to U-M Bioinformatics Graduate Program students and faculty.

"Bamnostic: a pure Python OS-agnostic BAM query toolset"

Abstract

The Binary Alignment Map (BAM) format is one of the most widely used formats for processing sequencing data. A C-level API library called htslib was developed in tandem to support the interrogation of BAM data. Many tools; such as samtools (written in C), picard (written in Java), and Pysam (written in Python) are just language-specific wrappers that provide an interface for htslib. However, because of this dependency, Pysam (the library of choice for Python developers working with BAM files) cannot be used in PyPy runtimes, small web applications, or Windows environments. Bamnostic is meant to alleviate that.

Bamnostic is written in pure Python with no dependencies outside of the standard library. It can process BAM files both serially and in a random access manner. Bamnostic can run in any version of Python from 2.7 on, as well as being fully compatible with PyPy. Lastly, bamnostic was developed from the ground up as a drop-in replacement for Pysam.