How to use whole genome sequencing for
monitoring of antimicrobial resistance in bacteria
Introduction
Application of whole genome sequencing (WGS) for antimicrobial susceptibility testing (AST) offers the
possibility to rapidly transform and improve our way of performing surveillance of antimicrobial resistance
(AMR) in view of the extensive information that can be obtained with a single assay.
At present, AST is performed by phenotypic methods by which bacteria in vivo is exposed to different
concentrations of selected antimicrobials. This allows definition of either the minimum antimicrobial
concentration at which bacterial growth is inhibited (MIC, minimum inhibitory concentration) or the
diameter of the zone of inhibition of bacterial growth around an antimicrobial-containing disc. The numerical
values obtained (either an MIC-value or an inhibition zone diameter) are interpreted according to a set of
criteria to classify isolates as susceptible or resistant to a specific antimicrobial. Although supported in
decades by available, comprehensive guidelines for performance and interpretation of AST (EUCAST, CLSI),
this approach still suffers of serious drawbacks, for example when defining MIC-values/inhibition zone
diameters for some bacteriostatic antimicrobials such as sulphonamides or when MIC-values/inhibition zone
diameters are close to breakpoint values for categorization of susceptibility/resistance. Furthermore, due to
practical reasons, each bacterial isolate can only be tested for susceptibility to a limited number of
antimicrobials.
WGS holds the promise to overcome most of the shortcomings of phenotypic AST and offers a prediction of
resistance in bacteria based on presence of known resistance mediating genes. However, definite evidence
for feasibility of AST by WGS is lacking for most bacterial species and some scientific and technical hurdles
need to be solved. These include knowledge gaps in the genetic basis of AMR and establishment of
harmonized quality control metrics in WGS-based AST.
Currently, several databases of AMR genes exist (ResFinder, ARIBA, SRST2, GeneFinder, and CARD etc.). These
databases perform differently in detection of AMR determinants but these differences are not immediately
evident to all users. Optimally, one single, public database of all known AMR genes and mutations should be
established, regularly updated, and strictly curated using minimum standards for the inclusion of new AMR
genes. This database should be organized by bacterial species and include predicted phenotypes associated
with the AMR genes.
Insufficient knowledge of AMR mechanisms is the major limiting factor in application of WGS for AST and
knowledge of the phenotype-genotype relationship differs according to bacterial species and antimicrobial
compound. The EU monitoring of AMR in zoonotic and commensal bacteria encompasses Salmonella spp.,
Escherichia coli, Campylobacter jejuni and C. coli, Enterococcus faecium and E. faecalis and mandates testing
of susceptibility to antimicrobials relevant to human and veterinary medicine (Decision 2013/652/EU).
According to this legislation, AST results should be interpreted using epidemiological cut-off values (ECOFFs),
which divide bacterial populations in two groups based on presence/absence of phenotypically detectable
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resistance mechanisms to any given antimicrobial (EUCAST). Overall, results from early reports show a good
correlation between genotypes and phenotypes but all these studies emphasize the need of further research
including larger number of isolates and better understanding of the molecular basis of resistance to specific
antimicrobials before routine application of WGS can be considered as a valid alternative to phenotypic
methods in programmes for surveillance of antimicrobial resistance.
Requirements for sequencing
On the laboratory part of WGS, several steps are crucial to obtain DNA of sufficient quantity and quality for
sequence analysis. Important measurements are:
WGS process Impact
DNA quality and quantity Poor quality or contaminant DNA can be detected. Contamination may
originate either from upstream handling of the bacterial isolates and
DNA purification or from the preparation and running of the DNA
samples on the sequencer.
Raw reads quality and quantity Used to infer the coverage of the bacterial genome and thereby
provide a QC of the sequencing quality.
Reference genome assembly Assembly – the formation of a draft genome sequence from raw reads
and/or de novo assembly quality can be evaluated to provide QC of data processing.
A brief introduction to some of the applied methods for DNA extraction, library preparation and available
genomic tools follows below.
DNA extraction methods
There are many available methods and kits for DNA extraction. Here are examples of some widely used
methods:
MagNA Pure (Roche) boilates for bacterial DNA extraction
The boilate method was developed for PCR templates, but DNA extracted from boilates has proven to be
suitable for the preparation of libraries for whole genome sequencing. The advantages of this method include
that there are no requirements for special equipment or reagents, preparation is rapid and it is safe to
transport pathogenic isolates for sequencing. MagNA Pure is an automated system for DNA extraction.
MagNA Pure LC 2.0 Instrument can perform a majority of the extraction steps, such as binding of DNA to
magnetic glass particles, washing steps, elution of pure DNA. The purified DNA may be analysed with respect
to DNA integrity, recovery, purity and ability to amplify target sequence with LightCycler® 480 and
LightCycler® Carousel-Based Instruments.
([Link]
[Link])
Easy-DNA™ Kit (Invitrogen) DNA extraction
This extraction method yields high-quality DNA with an average size between 100 kb and 200 kb, which is
suitable for PCR, DNA hybridization, genomic DNA library construction, and other applications. The extraction
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procedure contains only 4 steps with no special equipment required ([Link]
Assets/LSG/brochures/713_021456_easydnapr_bro.pdf)
QIAsymphony DNA Investigator Kit
DNA extraction can be carried out using an automated method to extract DNA from bacterial cells. The
QIAsymphony DNA Investigator Kit enables automated purification of genomic DNA from 1–96 samples, such
as swabs, filters, casework or crime-scene samples, and blood on the QIAsymphony SP. Purification is fast
and efficient, and purified DNA performs well in downstream analyses. This method requires QIAsymphony
SP/AS instrument.
([Link]
bcec58502f72&lang=en)
Sequencing method and library preparation
The Illumina sequencing platforms are widely used in many laboratories, and there are specific kits available
for library preparation for these platforms. The Illumina NexteraXT DNA library preparation manual is found
at:
[Link]
Genomic tools
A wide range of tools for genomic analysis is available online. A comprehensive list of tools can be found in
Appendix 1. Tools used for species identification (kmer-finder), assembly of genomes (SPAdes and Velvet)
and identification of AMR genes (ResFinder) are all available on [Link]
What is needed for quality control of WGS data?
Quality control (QC) is essential to guarantee accuracy and precision of results of any laboratory test,
including WGS. Sequences of poor quality can lead to major errors in AST by failing to reveal AMR genes or
mutations. Other sources of error may derive from contamination of the DNA and from erroneous data
handling.
At present, different QC parameters are available to control and standardize WGS procedures (CDC-PulseNet,
2015; Ellington et al. 2017). Although QC metrics for WGS are widely available, currently, no international
standards for QC-thresholds have been set, thus hampering data portability. Agreement on QC metrics and
minimum performance standards to ensure good quality of the entire WGS process from DNA isolation to
data analysis would facilitate early harmonization of analytical approaches and interpretative criteria for
WGS-based predictive AST, and only datasets that pass agreed QC metrics should be used in AST predictions.
A set of QC parameters for draft genome assembly and their explanation has been listed by the EUCAST
committee (Ellington et al. 2017).
Table 1 QC parameters for draft genome assembly (Ellington et al. 2017)
QC parameter Explanation
Number of reads Number of reads refers to sequence yield (the amount sequenced)
Average read length The average length of all reads, measured in base pairs.
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QC parameter Explanation
Number of reads mapped to reference The number of reads that map to a closed (finished) genome (same strain).
sequence
Proportion of reads mapped to reference The proportion of reads that map to a closed genome (same strain).
sequence (%)
Number of reads mapped to reference The number of reads that map to a closed chromosome (same strain).
chromosome
Proportion of reads mapped to reference The proportion of reads that map to a closed genome’s chromosome (same strain).
chromosome (%) This cannot exceed 100%.
Reads mapped to reference plasmids The number of reads that map to plasmids, if present.
Proportion of reads mapped to reference The proportion of reads that map to plasmids (if present) of the closed genomes.
plasmids (%) This cannot exceed 100%.
Depth of coverage, total DNA sequence Describes the number of times the sequenced base pairs cover the reference DNA.
Number of base pairs sequenced divided by the total size (both chromosome and
plasmids) of the closed genome (same strain), often expressed with an “x” (e.g. 30x).
A minimum depth of 30x is usually preferred.
Depth of coverage: chromosome As for total DNA coverage, but describes the number of base pairs sequenced
divided by the total size of the closed chromosome (same strain).
Depth of coverage: plasmid As for total DNA coverage, but describes the number of base pairs sequenced
divided by the total size of the closed plasmid (same strain).
Size of assembled genome Often used to identify contamination. If the calculated size of all the contigs in base
pairs exceeds that expected it could indicate more than one genome.
Size of assembled genome per total size of The proportion of contigs that map directly to the closed genome (same strain). This
DNA sequence (%) cannot exceed 100%.
Total number of contigs Generally, the total number of contigs assembled, <1000 contigs indicates good
quality. For organisms with genomes 5- 6 Mb in size then <100 contigs is (generally)
realistic.
Longest contig length The length of the longest contig.
Mean, median and standard deviation Mean, median and standard deviation of the contigs, used to evaluate quality
N50 The length for which the collection of all contigs of that length or longer contains at
least half of the sum of the lengths of all contigs, and for which the collection of all
contigs of that length or shorter also contains at least half of the sum of the lengths
of all contigs. N50 >15 000 normally indicates good quality, but minimum size of 30
000 bp is often preferred.
NG50 Helpful for comparisons between assemblies. As N50, except that 50% of the
genome size must be of the NG50 length or longer. Where the assembly size ≤ the
genome size then NG50 cannot exceed N50.
References
CLSI, Clinical and Laboratory Standards Institute. Available at: [Link]
CARD, the Comprehensive Antibiotic Resistance Database. Available at [Link]
CDC-PulseNet, Laboratory standard operating procedure for Pulse-Net Nextera XT library prep and run setup
for the Illumina MiSeq and Pulse-Net standard operating procedure for Illumina MiSeq data quality control.
Available at: [Link] and
[Link]
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Decision 2013/652/EU. Commission implementing decision of 12 November 2013 on the monitoring and
reporting of antimicrobial resistance in zoonotic and commensal bacteria.
Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MT,
Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM,
Samuelsen Ø, Woodford N; The role of whole genome sequencing in antimicrobial susceptibility testing of
bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect. 2017 Jan;23(1):2-22. doi:
10.1016/[Link].2016.11.012.
ENGAGE, Establishing next generation sequencing ability for genomic analysis in Europe. Further information:
[Link]
EUCAST, the European Committee on Antimicrobial Susceptibility Testing. [Link]
NCBI, the Bacterial Antimicrobial Resistance Reference Gene Database. Available at:
[Link]
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Appendix 1
Guideline to bioinformatics tools – ‘Availability, what to use – and when’
This document describes the most commonly used software and algorithms for processing whole
genome sequencing. It is divided into categories which describe the key processes for analysing short
read data.
The list was initially generated by ENGAGE (Establishing Next Generation Sequencing Ability for Genomic
Analysis in Europe, has received funding from European Food Safety Authority (EFSA), grant agreement
GP/EFSA/AFSCO/2015/01 (New approaches in identifying and characterizing microbiological and chemical
hazards)) and is adapted from [Link]
1. Quality Assessment and Trimming
This is the process by which the quality of fastq files is determined and subsequent optional trimming of
the data to trim or remove poor quality reads.
1.1. Trimmomatic
A flexible read trimming tool that will remove Illumina adapters, reads below a certain length and
low quality ends of the read (Windows, Mac OS X and Linux).
[Link]
Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bolger, Lohse & Usadel (2014).
Bioinformatics, btu170.
1.2. Seqtk
Tool for processing sequences in the FASTA or FASTQ that can be used for adapter removal and
trimming of low‐quality bases (Windows, Mac OS X and Linux).
[Link]
1.3. FastX
Toolkit for FASTQ and FASTA preprocessing that can be used for trimming, clipping, barcode splitting,
formatting and quality trimming (Windows, Mac OS X and Linux).
[Link]
1.4. FastQC
A quality control tool for assessing the quality of NGS data (Windows, Mac OS X and Linux)
[Link]
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2. Assembly
This is the process of joining short reads into longer contigs (contiguous lengths of DNA) without the
need for a reference sequence.
2.1. VelvetK
Perl script to estimate best k‐mer size to use for your Velvet de novo assembly (Windows, Mac OS X
and Linux).
[Link]
2.2. KmerGenie
Best k‐mer length estimator for single‐k genome assemblers like velvet (Windows, Mac OS X and
Linux).
Informed and Automated k‐Mer Size Selection for Genome Assembly. Chikhi & Medvedev HiTSeq
2013.
[Link]
2.3. Khmer
Set of command‐line tools for dealing with large and noisy datasets to normalise and scale the data
for more efficient genome assembly (Linux and Mac OS X)
The khmer software package: enabling efficient nucleotide sequence analysis. Crusoe et al., 2015.
F1000 [Link]
[Link]
2.4. Minia
Short‐read assembler based on a de Bruijn graph for low‐memory assembly (Windows, Mac OS X and
Linux).
Space‐efficient and exact de Bruijn graph representation based on a Bloom filter. Chikhi & Rizk.
Algorithms for Molecular Biology, BioMed Central, 2013, 8 (1), pp.22.
[Link]
2.5. SPAdes
Short and hybrid‐long read assembler based on a de Bruijn graph that also performs error correction
and is a multi‐k genome assembler (Mac OS X and Linux).
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single‐ Cell Sequencing.
Bankevich, Nurk, Antipov, Gurevich, Dvorkin, Kulikov, Lesin, Nikolenko, Pham, Prjibelski, Pyshkin,
Sirotkin, Vyahhi, Tesler, Alekseyev, and Pevzner. Journal of Computational Biology 19(5) (2012), 455‐
477. doi:10.1089/cmb.2012.0021
[Link]
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2.6. Velvet
De novo short read genome assembler with error correction to produce high quality unique contigs
(Linux).
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Zerbino and Birney.
Genome Res. May 2008 18: 821‐829; Published in Advance March 18, 2008,
doi:10.1101/gr.074492.107
[Link]
2.7. Canu
Long‐read assembler designed for high‐noise data such as that generated by PacBio or Oxford
Nanopore MinION. Canu also performs error correction (Windows, Mac OS X and Linux).
Canu: scalable and accurate long‐read assembly via adaptive k‐mer weighting and repeat
separation. Koren, Walenz, Berlin, Miller & Phillippy. doi:[Link]
[Link]
2.8. Bandage
Program for visualising de novo assembly graphs by displaying connection which are not present in
the contigs file for assembly assessment (Linux and Mac OS X).
Bandage: interactive visualization of de novo genome assemblies. Wick, Schultz, Zobel, and Holt.
Bioinformatics (2015) 31 (20): 3350‐3352 doi:10.1093/bioinformatics/btv383
[Link]
3. Annotation
The process which takes the raw sequence of contigs resulting from assembly and marks it with features
such as gene names and putative functions.
3.1. Prokka
Software tool for the rapid annotation of prokaryotic genomes (Windows, Mac OS X and Linux).
Prokka: rapid prokaryotic genome annotation. Seemann T. Bioinformatics. 2014 Jul 15;30(14):2068‐9.
PMID:24642063
[Link]
3.2. RAST
Fully‐automated service for annotating complete or nearly complete bacterial and archeal genomes
(Online tool).
The RAST Server: Rapid Annotations using Subsystems Technology. Aziz, Bartels, Best, DeJongh, Disz,
Edwards, Formsma, Gerdes, Glass, Kubal, Meyer, Olsen, Olson, Osterman, Overbeek, McNeil,
Paarmann, Paczian, Parrello, Pusch, Reich, Stevens, Vassieva, Vonstein, Wilke & Zagnitko. BMC
Genomics, 2008
[Link]
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3.3. Genix
Fully automated pipeline for bacterial genome annotation (Online tool).
[Link]
4. Alignment or sequence searching
Tools to align a sequence to other sequences locally or against publically available nucleotide or protein
archives.
4.1. BLAST
Search tool to find regions of similarity between biological sequences through alignment and
calculating statistical significance (Windows, Mac OS X and Linux)
Basic local alignment search tool. Altschul, Gish, Miller, Myers & Lipman. Journal of Molecular
Biology, Volume 215, Issue 3, 1990, Pages 403‐410
[Link]
4.2. MUMmer
A system for rapidly aligning entire genomes and finding matches in DNA sequences (Windows, Mac
OS X and Linux).
Versatile and open software for comparing large genomes. A.L. Delcher, A. Phillippy, J. Carlton, and
S.L. Salzberg, Nucleic Acids Research (2002), Vol. 30, No. 11 2478‐2483.
[Link]
4.3. Mega
Sophisticated and user‐friendly software suite for analysing DNA and protein sequence data from
species and populations (Windows, Mac OS X and Linux)
MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Kumar, Stecher &
Tamura (2016) Molecular Biology and Evolution 33:1870‐1874
[Link]
5. Mapping
Alignment of short reads against a reference sequence so that amount of coverage or variations
compared to the reference can be assessed.
5.1. BWA
Software package for mapping low‐divergent sequences against a large reference genome using the
Burrows‐Wheeler transform algorithm (Windows, Mac OS X and Linux).
Fast and accurate short read alignment with Burrows‐Wheeler Transform. Li H. and Durbin R. (2009)
Bioinformatics, 25:1754‐60. [PMID: 19451168]
[Link]
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5.2. Bowtie 2
Tool for aligning sequencing reads to long reference genomes also based on the Burrows‐Wheeler
transform algorithm (Windows, Mac OS X and Linux).
Fast gapped‐read alignment with Bowtie 2. Langmead & Salzberg. Nature Methods. 2012, 9:357‐359.
[Link]
5.3. Tablet
Lightweight, high‐performance graphical viewer for next generation sequence assemblies and
alignments that can be used to view mapping (Windows, Mac OS X and Linux).
Using Tablet for visual exploration of second‐generation sequencing data. Milne I, Stephen G, Bayer
M, Cock PJA, Pritchard L, Cardle L, Shaw PD and Marshall D. 2013. Briefings in Bioinformatics 14(2),
193‐202.
[Link]
6. Variant Calling
6.1. SAMtools
Toolkit that provides various utilities for manipulating alignments in the SAM format and also can be
used generating consensus sequences and variant calling (Windows, Mac OS X and Linux).
The Sequence alignment/map (SAM) format and SAMtools. Li*, Handsaker*, Wysoker, Fennell, Ruan,
Homer, Marth, Abecasis, Durbin and 1000 Genome Project Data Processing Subgroup (2009)
Bioinformatics, 25, 2078‐9. [PMID: 19505943]
[Link]
6.2. GATK
Toolkit with a primary focus on variant discovery and genotyping (Windows, Mac OS X and Linux).
The Genome Analysis Toolkit: A MapReduce framework for analyzing next‐generation DNA
sequencing data. McKenna, Hanna, Banks, Sivachenko, Cibulskis, Kernytsky, Garimella, Altshuler,
Gabriel, Daly & DePristo. Genome Res. September 2010 20: 1297‐1303; doi:10.1101/gr.107524.110
[Link]
6.3. Picard
A set of command line tools (in Java) for manipulating high‐throughput sequencing data and formats
(Windows, Mac OS X and Linux).
[Link]
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7. Phylogenetic analysis
Assessment of the evolutionary relationship between samples using either distance‐based or Bayesian
methodologies.
7.1. RaxML
Randomized Axelerated Maximum Likelihood program for sequential and parallel Maximum
Likelihood based inference of large phylogenetic trees (Windows, Mac OS X and Linux).
RAxML Version 8: A tool for Phylogenetic Analysis and Post‐Analysis of Large Phylogenies. A.
Stamatakis. Bioinformatics (2014) 30 (9): 1312‐1313.
[Link]
FastTree
Faster tool for speedy inference of approximately‐maximum‐likelihood phylogenetic trees from
alignments of nucleotide or protein sequences (Windows, Mac OS X and Linux).
FastTree: Computing Large Minimum‐Evolution Trees with Profiles instead of a Distance Matrix.
Price, Dehal & Arkin (2009). Molecular Biology and Evolution 26:1641‐1650,
doi:10.1093/molbev/msp077.
[Link]
7.2. CSI Phylogeny
Tool to call SNPS, filters the SNPs, do site validation and inference of phylogeny through a graphical
user interface (Online tool).
Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms.
Kaas, Leekitcharoenphon, Aarestrup & Lund. PLoS ONE 2014; 9(8): e104984.
[Link]
7.3. Harvest
Suite of core‐genome alignment and visualization tools for quickly analysing thousands of
intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic
trees (Windows, Mac OS X and Linux).
The Harvest suite for rapid core‐genome alignment and visualization of thousands of intraspecific
microbial genomes. Treangen, Ondov, Koren & Phillippy. Genome Biology, 15 (11), 1‐15
[Link]
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7.4. Gubbins
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that
iteratively identifies loci containing elevated densities of base substitutions while concurrently
constructing a phylogeny based on the putative point mutations outside of these regions (Windows,
Mac OS X and Linux).
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences
using Gubbins. Croucher, Page, Connor, Delaney, Keane, Bentley, Parkhill, Harris , Nucleic Acids
Research, 2014. doi:10.1093/nar/gku1196
[Link]
7.5. BEAST
Cross‐platform program for Bayesian analysis of molecular sequences using MCMC (Windows, Mac
OS X and Linux).
Bayesian phylogenetics with BEAUti and the BEAST 1.7. Drummond, Suchard, Xie & Rambaut (2012)
Molecular Biology And Evolution 29: 1969‐1973.
[Link]
7.6. FigTree
A graphical viewer of phylogenetic trees and program for producing publication‐ready figures of
trees (Windows, Mac OS X and Linux).
[Link]
8. Virulence and antimicrobial resistance gene prediction
Inference of potential for a virulent phenotype or resistance to an antimicrobial based on nucleotide
sequence
8.1. PathogenFinder
Web‐server for the prediction of bacterial pathogenicity by analysing the input proteome, genome,
or raw reads provided by the user (Online tool).
PathogenFinder ‐ Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data.
Cosentino, Larsen, Aarestrup & Lund (2013) PLoS ONE 8(10): e77302.
[Link]
8.2. ResFinder
Web‐server that identifies acquired antimicrobial resistance genes in total or partial sequenced
isolates of bacteria (Online tool).
Identification of acquired antimicrobial resistance genes. Zankari, Hasman, Cosentino, Vestergaard,
Rasmussen, Lund, Aarestrup & Larsen (2012) J Antimicrob Chemother.
[Link]
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9. Species identification
9.1. Kraken
System for assigning taxonomic labels to short DNA sequences, usually obtained through
metagenomics studies (Linux).
Kraken: ultrafast metagenomic sequence classification using exact alignments. Wood & Salzberg
(2014) Genome Biology, 15:R46.
[Link]
10. Comparative genomic tools
Comparison of multiple genomes to determine regions of similarity or difference either on a gene‐by
gene basis or across the whole genome.
10.1. BEDTools
Toolkit for the manipulation of genome data for genomic analysis tasks on genomic intervals from
multiple files (Mac OS X and Linux)
BEDTools: a flexible suite of utilities for comparing genomic features. Quinlan & Hall (2010)
Bioinformatics 26 (6) doi:10.1093/bioinformatics/btq033
[Link]
10.2. Roary
High speed stand‐alone pan genome pipeline, which takes annotated assemblies in GFF3 format and
calculates the pan genome (Windows, Mac OS X and Linux).
Roary: Rapid large‐scale prokaryote pan genome analysis. Page, Cummins, Hunt, Wong, Reuter,
Holden, Fookes, Falush, Keane & Parkhill (2015) Bioinformatics; 31(22):3691‐3693.
doi:10.1093/bioinformatics/btv421
[Link]
10.3. Mauve
Interactive genome alignment software that allows for easy browsing of multiple genomes to look for
similarities and differences (Windows, Mac OS X and Linux).
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. Darling, Mau,
Blattner, & Perna (2004) Genome Res. 1394‐1403; doi:10.1101/gr.2289704
[Link]
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10.4. ACT
Java application for displaying pairwise comparisons between two or more DNA sequences and
allowing browsing of detailed annotation (Windows, Mac OS X and Linux).
ACT: the Artemis Comparison Tool. Carver, Rutherford, Berriman, Rajandream, Barrell & Parkhill
(2005) Bioinformatics;21;16;3422‐3 DOI: 10.1093/bioinformatics/bti553
[Link]
10.5. BRIG
Image generating software that displays circular blast comparisons between a large number of
genomes or DNA sequences (Windows, Mac OS X and Linux).
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons (2011) Alikhan, Petty,
Zakour & Beatson. BMC Genomics, 12:402. PMID: 21824423
[Link]
10.6. EasyFig
Python application for creating linear comparison figures of multiple genomic loci with an easy‐to‐
use graphical user interface (GUI) (Windows, Mac OS X and Linux).
Easyfig: a genome comparison visualiser. Sullivan, Petty & Beatson (2011) Bioinformatics; 27 (7):
1009‐[Link]: 21278367
[Link]
10.7. SeqFindR
Tool to easily create informative genomic feature plots by detecting the presence or absence of
genomic features from a database in a set of genomes. If infrastructure is not available the cloud
based services are worth considering (Mac OS X and Linux)
[Link]
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