Mingle: A Command Line Utility for Merging Multi-fasta Files

Journal of computational biology: A journal of computational molecular cell biology

LuigiMarongiu^1,2¹  HeikeAllgayer^2² 

[1] Address correspondence to: Dr. Luigi Marongiu, Department of Experimental Surgery–Cancer Metastasis, Medical Faculty Mannheim, Centre for Biomedicine and Medical Technology Mannheim (CBTM), Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Str. 6, Mannheim 68135, Germany^1;Department of Experimental Surgery–Cancer Metastasis, Medical Faculty Mannheim, Centre for Biomedicine and Medical Technology Mannheim (CBTM), Ruprecht-Karls University of Heidelberg, Mannheim, Germany^2

关键词: alignment;    fasta;    genome;    reference;    sequencing;   

DOI  :  10.1089/cmb.2018.0243

学科分类：生物科学（综合）

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

Massively parallel sequencing (MPS) has become a standard technique in molecular biology whose application has spread from the analysis of the human genome to that of virtually all other organisms. MPS requires reference genomes to be performed and, in some cases, multiple genomes need to be handled as a single unit to carry out genetic analysis. Nucleic acid sequences are typically stored in “fasta” files, which can contain multiple genomes (“multi-fasta”). Although it is possible to convert a multi-fasta file into a single sequence using specific computer commands, the resulting file will not keep track of the boundaries of the original sequences, making it difficult to determine to what genome read obtained from MPS belong to. In this study we introduce mingle, a shell script that can be used to create custom reference genome by merging multi-fasta files while providing a list of boundaries of the individual genomes that can be used for downstream analysis.

【 授权许可】

Unknown