Reference-free detection of isolated SNPs

Reference-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...

Reference - free detection of isolated SNPs Additional File 1

1University of Bordeaux, CNRS / LaBRI, F-33405 Talence, France, 2University of Bordeaux, CBiB, F-33000 Bordeaux, France, 3INRA, UMR1349 IGEPP, Le Rheu, France, 4GenScale, INRIA Rennes Bretagne-Atlantique, IRISA, Rennes, France, 5BAMBOO, INRIA Grenoble Rhone-Alpes, Lyon, France, 6Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1 UMR CNRS 5558, Lyon, France, 7INRA, UMR1300 Biology...

Identifying 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...

Stable SNPs in malaria antigen genes in isolated populations.

Detection of CTX-M-β Lactamases form Isolated Klebsiella pneumoniae

  Background and Objective: Organisms producing CTX-M β-lactamases are emerging as a source of resistance to oxyiminocefalosporins such as ceftriaxone and ceftazidime. However, the laboratory detection of these strains is not well defined. In this study, phenotypic assay for screening of extended-spectrum β-lactamases producing strains and molecular assay for the identification of CTX-M β-lact...