Comparison of classical multi-locus sequence typing software for next-generation sequencing data
نویسندگان
چکیده
منابع مشابه
Comparison of classical multi-locus sequence typing software for next-generation sequencing data
Multi-locus sequence typing (MLST) is a widely used method for categorizing bacteria. Increasingly, MLST is being performed using next-generation sequencing (NGS) data by reference laboratories and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have c...
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MOTIVATION The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant in many biomedical applications. While next-generation sequencing data are often available for a patient, deducing the HLA genotype is difficult because of substantial sequence similarity within the cluster and exceptionally high variability of the loci. Established approache...
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Next generation sequencing (NGS) has been leading the genetic study of human disease into an era of unprecedented productivity. Many bioinformatics pipelines have been developed to call variants from NGS data. The performance of these pipelines depends crucially on the variant caller used and on the calling strategies implemented. We studied the performance of four prevailing callers, SAMtools,...
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Introduction: The precision and time required for analysis of data in next-generation sequencing (NGS) depends on many factors including the tools utilized for alignment, variant calling, annotation and filtering of variants, personnel expertise in data analysis and interpretation, and computational capacity of the lab and its optimization is a challenging task. Method: An application software...
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ژورنال
عنوان ژورنال: Microbial Genomics
سال: 2017
ISSN: 2057-5858
DOI: 10.1099/mgen.0.000124