Quality control assessment for microbial genomes: GalaxyTrakr MicroRunQC workflow v3

Abstract

PURPOSE: Step-by-step instructions for checking WGS sequence quality. The MicroRunQC workflow, implemented in a custom Galaxy instance, will produce quality assessments for raw reads (Illumina paired-end fastq files) and draft de novo assemblies, along with reporting the sequence type for each isolate. This workflow will work on most microbial pathogens, so we advise laboratories to upload their entire MiSeq/NextSeq run through this workflow. SCOPE: This protocol covers the following tasks: 1. set up an account in GalaxyTrakr 2. Create a new history/workspace 3. Upload data 4. Execute the MicroRunQC workflow 5. Interpret the results V3: updated with Cronobacter thresholds

Draft Genome Sequences of 110 Shiga Toxin-Producing Escherichia coli Isolates Collected from Bovine Manure Samples in the Southern United States

“…Taxonomy assignments were verified using Kraken ( 14 ). Sequencing records with quality metrics above minimum thresholds accessed by the “MicroRunQC v1” workflow ( 15 ) and correctly identified as E. coli were submitted to NCBI. MicroRunQC is a galaxy quality-control (QC) workflow that includes FastQC ( 15 ), assembly QC, and multilocus sequence typing (MLST).…”

“…Sequencing records with quality metrics above minimum thresholds accessed by the “MicroRunQC v1” workflow ( 15 ) and correctly identified as E. coli were submitted to NCBI. MicroRunQC is a galaxy quality-control (QC) workflow that includes FastQC ( 15 ), assembly QC, and multilocus sequence typing (MLST). Genomes were annotated automatically upon upload using NCBI Prokaryotic Genome Annotation Pipeline ( 16 ).…”

Characteristics of antimicrobial resistance inEscherichia coliisolated from retail meat products in North Carolina

“…Briefly, 0.3 ng/μl of DNA from each E. coli isolate was pooled together and sequenced on an Illumina MiSeq platform (Illumina, San Diego, CA) using 2 x 250 or 2 x 300 paired-end approach. The raw paired end reads from the sequencer were demultiplexed and submitted to the NCBI database where they were assigned an accession number [21]. (https://cge.food.dtu.dk/services/MobileElementFinder/) [22].…”

Draft Genome Sequences of 278 Salmonella enterica Isolates from Poultry Litter in the Southeastern United States

“…Sequencing records with quality metrics above GenomeTrakr ( 19 , 20 ) thresholds and correctly identified as S. enterica were submitted to the NCBI. Quality control thresholds for Salmonella are an average coverage of ≥30×, average read quality ( Q ) scores for reads 1 and 2 of ≥30, a sequence length of 4.3 to 5.2 Mbp, and a number of contigs of ≤300 ( 20 ). Salmonella serotypes were predicted using SeqSero2 v1.1.0 ( 21 ).…”