The GMI proficiency test (PT) is provided to facilitate harmonization and standardization in whole genome sequencing and data analysis, with the aim to produce comparable data for the GMI initiative and represents an important tool for the evaluation and production of reliable laboratory results of consistently good quality within the area of DNA preparation, sequencing, and analysis (e.g. clustering).
The below reports present the results based on the proficiency tests launched by GMI working group 4.In the reports, individual results are summarized and analyzed.
The main objective of this proficiency test (PT) was to facilitate the production of reliable laboratory results of consistently good quality within the area of whole genome sequencing (WGS) related to Campylobacter spp., Listeria monocytogenes, and Klebsiella pneumoniae.
The objective of the dry-lab component was to assess the differences among laboratories in the detection of variants (e.g., single nucleotide polymorphisms (SNPs)) from the analysis of whole genome sequence data. Participants were provided three datasets and asked to analyze them with the current protocol implemented in their lab for detecting such variants. In addition to answering an online survey regarding the type of analysis the participant performed, the participant also submitted a fasta formatted matrix of variants and a newick formatted tree file.
This document describes the analysis of those three source of data - the survey, fasta matrix, and newick tree file.
The objective of the dry-lab component was to assess the differences among laboratories in the detection of variants (e.g., single nucleotide polymorphisms (SNPs)) from the analysis of whole genome sequence data. Participants were provided three datasets and asked to analyze them with the current protocol implemented in their lab for detecting such variants. In addition to answering an online survey regarding the type of analysis the participant performed, the participant also submitted a fasta formatted matrix of variants and a newick formatted tree file.
This document describes the analysis of those three source of data - the survey, fasta matrix, and newick tree file.
The main objective of this pilot proficiency test (PT) was to facilitate the production of reliable laboratory results of consistently good quality within the area of whole genome sequencing (WGS). The results presented in this report were part of a pilot PT that was initiated as a ‘test run’ to allow for collection of experience with the purpose of adjusting documentation and/or the practical approach before the full roll-out of the PT, scheduled to be launched to a global audience in 2015.