Nanopore sequencing of poliovirus Isolates analysis and quality control checks v2

Le résumé fourni par la source

This standard operating procedure indicates how to perform data analysis, quality control checks, and data reporting after nanopore sequencing of poliovirus isolates and provides guidance on best practice for ensuring relevant sequencing run data are recorded. Procedure For isolate sequencing results to be valid and suitable for reporting, sufficient sample metadata must be recorded and data integrity maintained throughout the planning stage of the experiment, during the experiment and after the experiment. Quality control checks have been included to ensure that the protocol has been performed correctly and that results are valid. Later comparison of the poliovirus isolates sequencing results with culture-based poliovirus detections can be facilitated by adding further metadata describing the timelines and results for processing of the same samples by cell-culture. An overview of the procedure is shown in Figure 1. It is the responsibility of the Lab senior scientist to designate staff to conduct the QC analysis report and to ensure that the personnel conducting the data analysis has provided complete and accurate data, and the report generated is correct prior to approval. Data must be reviewed and approved by the lab senior scientist before QC analysis review with the technical team (PSC member). The designated technical team lead then submits the QC’d data to the GSL for review/approval. Once approved, the GSL share the QC'd data to the program. A log should be kept of the sequencing runs that are performed, indicating whether all quality control checks have been completed or whether some remain pending, and confirming that all reportable sequences have been reported. All VP1 poliovirus sequences generated (even in cases of sample or run QC fail) should be collected into a laboratory sequence QC database folder to aid in the identification of contamination. This addition can be performed by annotating the vp1_sequence.fasta from a run with the run name (e.g. "vp1_sequences_Run21.fasta") and copying it into the database folder. We recommend that you do not add RNA from stool surveillance to the same run. The RNA from cell-culture will be much more concentrated, resulting in the distribution of sequencing data skewing towards the isolate samples rather than the stool samples.

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.