Principles of Effective SNP Filtering for Molecular Ecologists

This set of flashcards covers key concepts and terminology related to SNP filtering methodologies discussed in the lecture notes.

SNP (Single Nucleotide Polymorphism)

A variation at a single position in a DNA sequence among individuals.

RAD-seq (Restriction site-associated DNA sequencing)

A cost-efficient method used for identifying SNPs by sequencing fragments around restriction enzyme cut sites.

Bioinformatics

The application of computer technology to manage and analyze biological data, particularly in genomics.

Artefact

An erroneous observation or result that is introduced during the experimental or analytical process.

Genotyping error

Mistakes in determining the genotype of an organism, often due to poor-quality data or inadequate methodologies.

Coverage effects

Variability in the representation of alleles in a sequencing run, often resulting from insufficient sequencing depth.

De novo assembly

The process of assembling sequences from scratch without a reference genome.

Library preparation

The process of preparing DNA fragments for sequencing, which includes steps like fragmentation, adapter ligation, and amplification.

PCR artefact

Errors related to polymerase chain reaction, such as chimeras or preferential amplification of certain fragments.

Linkage disequilibrium

Non-random association of alleles at different loci in a given population.

Quality control measures

Procedures implemented to ensure the quality and reliability of data collected during experiments.

Filtering strategies

Methods applied to data sets to remove low-quality data or artefacts to improve data reliability and accuracy.