SRAMM: Short Read Alignment Mapping Metrics

Autor: Alvin Chon, Xiaoqiu Huang
Rok vydání: 2021
Předmět:
Zdroj: International Journal on Bioinformatics & Biosciences. 11:01-07
ISSN: 1839-9614
DOI: 10.5121/ijbb.2021.11201
Popis: 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.
Comment: 7 pages, 2 figures
Databáze: OpenAIRE
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