SRAMM: Short Read Alignment Mapping Metrics
Autor: | Alvin Chon, Xiaoqiu Huang |
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Rok vydání: | 2021 |
Předmět: |
Genomics (q-bio.GN)
Information retrieval Downstream (software development) Computer science business.industry media_common.quotation_subject Process (computing) Python (programming language) Short read Software FOS: Biological sciences Quantitative Biology - Genomics Quality (business) Line (text file) MIT License business computer media_common computer.programming_language |
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 |
Externí odkaz: |
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