منابع مشابه
Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes
Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these species have provided unique insights into mammalian gene function. However, the number of spec...
متن کاملIdentifying SNPs without a Reference Genome by Comparing Raw Reads
Next generation sequencing (NGS) technologies are being applied to many fields of biology, notably to survey the polymorphism across individuals of a species. However, while single nucleotide polymorphisms (SNPs) are almost routinely identified in model organisms, the detection of SNPs in non model species remains very challenging due to the fact that almost all methods rely on the use of a ref...
متن کاملSNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot be applied to non-model species. They are also mostly tailored for whole genome (re-)sequencing experiments, wher...
متن کاملExploring genome characteristics and sequence quality without a reference
MOTIVATION The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly. RESULTS This article addresses the practical aspects of de novo assembly by introducing new ways to perform qua...
متن کاملReference-free detection of isolated SNPs
Detecting single nucleotide polymorphisms (SNPs) between genomes is becoming a routine task with next-generation sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2010
ISSN: 1471-2105
DOI: 10.1186/1471-2105-11-130