Sramm: short read alignment mapping metrics

TL;DR

SRAMM is a versatile command line tool that provides enhanced metrics, filtering, and visualization for short read alignments, improving post-alignment analysis for various applications.

Contribution

It introduces a new tool that generates multiple mapping scores and metrics, standardizing and streamlining post-alignment evaluation for short read data.

Findings

Provides multiple concept-based mapping scores

Compatible with all aligners producing SAM/BAM/CRAM files

Facilitates efficient filtering and visualization of alignments

Abstract

Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods generally are neither standardized nor well described in literature or software manuals. Additionally, third party mapping quality programs are typically computationally intensive or designed for specific applications. SRAMM efficiently generates multiple different concept-based mapping scores to provide for an informative post alignment examination and filtering process of aligned short reads for various downstream applications. SRAMM is compatible with Python 2.6+ and Python 3.6+ on all operating systems. It works with any short read aligner that generates SAM/BAM/CRAM file outputs and reports 'AS' tags. It is freely available under the MIT license at http://github.com/achon/sramm.