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

Luigi Marongiu1, Heike Allgayer1

  • 1Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Centre for Biomedicine and Medical Technology Mannheim (CBTM), Ruprecht-Karls University of Heidelberg, Mannheim, Germany.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|February 15, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces mingle, a script for merging multiple fasta genome files into a single reference genome. It preserves individual genome boundaries for accurate downstream analysis in massively parallel sequencing (MPS).

Keywords:
alignmentfastagenomereferencesequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Massively parallel sequencing (MPS) is a standard molecular biology technique requiring reference genomes.
  • Handling multiple genomes within a single file (multi-fasta) is common for genetic analysis.
  • Existing methods for merging multi-fasta files lose track of individual genome boundaries.

Purpose of the Study:

  • To introduce a novel shell script named 'mingle' for creating custom reference genomes.
  • To address the challenge of merging multi-fasta files while retaining individual sequence information.
  • To facilitate downstream analysis in MPS by providing genome boundary data.

Main Methods:

  • Development of a shell script ('mingle') to process multi-fasta files.
  • Merging multiple genomes into a single reference sequence.
  • Generating a list of boundaries for each original genome within the merged file.

Main Results:

  • The 'mingle' script successfully merges multi-fasta files into a single reference genome.
  • The script accurately records the boundaries of the individual genomes.
  • The output facilitates the assignment of MPS reads to their original genomes.

Conclusions:

  • 'mingle' provides a practical solution for managing and utilizing multi-genome references in MPS.
  • The script enhances the accuracy and efficiency of genetic analyses involving multiple organisms.
  • This tool supports a wide range of genomic research applications.