ArticleMicrobial informatics and experimentation2013
Beginner's guide to comparative bacterial genome analysis using next-generation sequence data.
Article in Microbial informatics and experimentation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed, 144 citations in OpenAlex.
- Benchmarking pangenome dynamics and horizontal gene transfer inFrontiers in microbiology · 2025Article
- De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome.BMC genomics · 2024Article
- Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut.Applied and environmental microbiology · 2022Review
- Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates.Veterinary research · 2022Article
- Computational approaches to understanding Clostridioides difficile metabolism and virulence.Current opinion in microbiology · 2022Review
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Article
- A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses.Microorganisms · 2021Review
- Complete microbial genomes for public health in Australia and the Southwest Pacific.Microbial genomics · 2020Article
- Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients - a systematic review.Journal of oral microbiology · 2020Review
- Microbial Diversity in Deep-Subsurface Hot Brines of Northwest Poland: from Community Structure to Isolate Characteristics.Applied and environmental microbiology · 2020Article
- Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.BMC bioinformatics · 2020Article
- A workflow for generating multi-strain genome-scale metabolic models of prokaryotes.Nature protocols · 2020Article
- Article
- Comparative Analysis ofToxins · 2019Article
- Fine-Tuning of σJournal of bacteriology · 2019Article
- Article
- Methods for automatic reference trees and multilevel phylogenetic placement.Bioinformatics (Oxford, England) · 2019Article
- Comparative genome analysis of 15 clinicalAIMS microbiology · 2019Article
- Characterization and Bio-Typing of Multidrug Resistance Plasmids From UropathogenicFrontiers in microbiology · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High throughput sequencing is now fast and cheap enough to be considered part of the toolbox for investigating bacteria, and there are thousands of bacterial genome sequences available for comparison in the public domain. Bacterial genome analysis is increasingly being performed by diverse groups in research, clinical and public health labs alike, who are interested in a wide array of topics related to bacterial genetics and evolution. Examples include outbreak analysis and the study of pathogenicity and antimicrobial resistance. In this beginner's guide, we aim to provide an entry point for individuals with a biology background who want to perform their own bioinformatics analysis of bacterial genome data, to enable them to answer their own research questions. We assume readers will be familiar with genetics and the basic nature of sequence data, but do not assume any computer programming skills. The main topics covered are assembly, ordering of contigs, annotation, genome comparison and extracting common typing information. Each section includes worked examples using publicly available E. coli data and free software tools, all which can be performed on a desktop computer.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.