Dave says:

SPAdes (http://bioinf.spbau.ru/spades) is a new(ish) genome assembly program that is particularly suitable for assembly of bacterial genomes. SPAdes makes a number of improvements on the de Bruijn graph algorithms used by assemblers like Velvet, IDBA and SOAPdenovo, including iteration over values of kmer sizes, and incorporation of paired kmers (k-bimers), which allows information from paired end reads to be introduced into the computation at an earlier stage.

In their paper, the authors of SPAdes make comparisons with a number of popular assemblers using single-cell and multi-cell E. coli datasets. Their results show that SPAdes can in fact deliver better assemblies, with a higher N50 length and larger contigs. Since we regularly use Velvet for assembly, we wanted to perform some further comparisons between Velvet and SPAdes on the types of data sets we typically deal with. To this end we ran SPAdes and Velvet on 114 Shigella sonnei 54 bp paired end Illumina read sets (from our 2012 paper, reads available at ERP000182), and 67 unpaired 37 bp Staphylococcus aureus samples (from Harris 2010, available at ERP000070). We then calculated the N50, length, L50, the number of contigs > 500 bp, and the total contig length produced by each assembler. The figures below show the distributions of each of these values for the two data sets.

Shigella sonnei assemblies. Dark = SPAdes; light = Velvet Optimizer

Staphylococcus aureus assemblies. Dark = SPAdes; light = Velvet Optimizer.

There’s a few things to notice about these plots. Firstly there’s quite a bit of difference between the S. shigella and the S. aureus assembly statistics, although this is hardly surprising given that the S. sonnei reads are paired ends, while the S. aureus are unpaired (and only 37 bp long). What’s apparent though is that SPAdes and Velvet perform similarly on the S. aureus reads, but have very different performance on the S. sonnei reads, where SPAdes clearly outperforms Velvet. We can probably attribute this to the fact that SPAdes includes an improved algorithm for handling paired end reads.

For both species, SPAdes frequently results in a higher N50 than Velvet and a larger total contig length. For the paired end S. sonnei reads SPAdes also results in a larger number of contigs greater than 500 bp in length. For the L50 metric, Velvet results in quite low scores for the S. sonnei reads, with 10 or less contigs frequently accounting for at least half of the total contig size. However, given the total contig length obtained using SPAdes, the much higher values for L50 obtained using SPAdes are not unexpected.

In our current assembly pipeline, we run Velvet Optimizer a number of times using smaller and smaller steps for k in order to hone in on an optimal value. Using SPAdes, not only is this step incorporated into the assembly program, but the information from each iteration is combined to produce the final output. Thus SPAdes is able to capture the information obtained using small, highly sensitive kmer sizes, as well as large, highly specific, kmer sizes, and at the same time simplify our assembly pipeline. We’re currently beginning a new project looking at the pan-genome of a number of bacterial species, and we anticipate that this project will involve quite a bit of assembly. Based on the results shown above, and the pipeline process for SPAdes, it looks like we’ll be using SPAdes to do the bulk of this work.

Run specifics:

• Velvet was run on the S. sonnei pared end reads using VelvetOptimser with a minimum kmer size of 29 and a maximum kmer size of 89.
• SPAdes was run on the S. sonnei pared end reads using the default settings.
• Velvet was run on the S. sonnei pared end reads using VelvetOptimser with a minimum kmer size of 15 and a maximum kmer size of 35.
• SPAdes was run on the S. sonnei pared end reads using the kmer sizes of 15, 23, 35.

Today we came across a tool that can do the job: sam-stats from the ea-utils fastq processing package.

Getting the statistics is easy:

sam-stats -A -B aln.bam > aln-stats.txt

(The ‘A’ option turns on reporting for all ‘chromosomes’, whilst ‘B’ tell the program the file is a BAM)

The details of the output can be found on the sam-stats wiki page. There you can also find more options for statistics, as well as utilities for removing adapter sequences and de-multiplexing fastqs.

The idea for this came from discussions at last year’s ASM (Australian Society of Microbiology) meeting, where it was highlighted that there was a lack of courses and tutorials available for biologists to learn the basics of genomic analysis so that they can make use of next gen sequencing. Michael Wise, a founding editor of BMC Microbial Informatics and Experimentation based at UWA in Perth, suggested the new journal would be an ideal home for such a tutorial… so here we are:

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data

http://www.microbialinformaticsj.com/content/3/1/2/

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.

Four great tools

In the paper and tutorial, we introduce the four tools which we rely on most for basic analysis of bacterial genome assemblies: Velvet, ACT, Mauve and BRIG. All except ACT were developed as part of a PhD project, and have endured well beyond the original PhD to become well-known bioinformatics tools. New students take note!

In the paper, each tool is highlighted in its own figure, which includes some basic instructions. This is reproduced below, but is covered in much more detail in the tutorial that comes with the paper (link at the bottom).

1. Velvet for genome assembly

Possibly the most popular and widely used short read assembler, developed by the amazing Dan Zerbino during his PhD at EBI in Cambridge. Quite a PhD project!

[ Download | Paper | Protocol ]

Reads are assembled into contigs using Velvet and VelvetOptimiser in two steps, (1) velveth converts reads to k-mers using a hash table, and (2) velvetg assembles overlapping k-mers into contigs via a de Bruijn graph. VelvetOptimiser can be used to automate the optimisation of parameters for velveth and velvetg and generate an optimal assembly. To generate an assembly of E. coli O104:H4 using the command-line tool Velvet:

• Download Velvet [23] (we used version 1.2.08 on Mac OS X, compiled with a maximum k-mer length of 101 bp)

• Download the paired-end Illumina reads for E. coli O104:H4 strain TY-2482 (ENA accession SRR292770)

• Convert the reads to k-mers using this command:

velveth out_data_35 35 -fastq.gz -shortPaired -separate SRR292770_1.fastq.gz SRR292770_2.fastq.gz

• Then, assemble overlapping k-mers into contigs using this command:

velvetg out_data_35 -clean yes -exp_cov 21 -cov_cutoff 2.81 -min_contig_lgth 200

This will produce a set of contigs in multifasta format for further analysis. See Additional file 1: Tutorial for further details, including help with downloading reads and using VelvetOptimiser.

2. ACT for pairwise genome comparison

Part of the Sanger Institute’s Artemis suite of tools. Also look at Artemis (single genome viewer), DNA Plotter (which can draw circular diagrams of your genomes) and BAMView (which can display mapped reads overlaid on a reference genome), they are all available here.

[ Download | Paper | Manual ]

Artemis and ACT are free, interactive genome browsers (we used ACT 11.0.0 on Mac OS X).

• Open the assembled E. coli O104:H4 contigs in Artemis and write out a single, concatenated sequence using File -> Write -> All Bases -> FASTA Format.

• Generate a comparison file between the concatenated contigs and 2 alternative reference genomes using the website WebACT.

• Launch ACT and load in the reference sequences, contigs and comparison files, to get a 3-way comparison like the one shown here.

Here, the E. coli O104:H4 contigs are in the middle row, the enteroaggregative E. coli strain Ec55989 is on top and the enterohaemorrhagic E. coli strain EDL933 is below. Details of the comparison can be viewed by zooming in, to the level of genes or DNA bases.

3. Mauve for contig ordering and multiple genome comparison

Developed by the wonderful Aaron Darling during his PhD, he is now Associate Professor at University of Technology Sydney. Also see Mauve Assembly Metrics, an optional plugin for assessing assembly quality which was developed for the Assemblathon.

[ Download | Paper | User Guide ]

Mauve is a free alignment tool with an interactive browser for visualising results (we used Mauve 2.3.1 on Mac OS X).

• Launch Mauve and select File -> Align with progressiveMauve

• Click ‘Add Sequence…’ to add your genome assembly (e.g. annotated E. coli O104:H4 contigs) and other reference genomes for comparison.

• Specify a file for output, then click ‘Align…’

• When the alignment is finished, a visualization of the genome blocks and their homology will be displayed, as shown here. E. coli O104:H4 is on the top, red lines indicate contig boundaries within the assembly. Sequences outside coloured blocks do not have homologs in the other genomes.

4. BRIG (BLAST Ring Image Generator) for multiple genome comparison

From Nabil-Fareed Alikhan at the University of Queensland, also as part of a graduate project, which I believe is still in progress…

[ Download | Download BLAST | Paper | Tutorial ]

BRIG is a free tool that requires a local installation of BLAST (we used BRIG 0.95 on Mac OS X). The output is a static image.

• Launch BRIG and set the reference sequence (EHEC EDL933 chromosome) and the location of other E. coli sequences for comparison. If you include reference sequences for the Stx2 phage and LEE pathogenicity island, it will be easy to see where these sequences are located.

• Click ‘Next’ and specify the sequence data and colour for each ring to be displayed in comparison to the reference.

• Click ‘Next’ and specify a title for the centre of the image and an output file, then click ‘Submit’ to run BRIG.

• BRIG will create an output file containing a circular image like the one shown here. It is easy to see that the Stx2 phage is present in the EHEC chromosomes (purple) and the outbreak genome (black), but not the EAEC or EPEC chromosomes.

Tutorial

The tutorial accompanying the article is available here. To give you an idea of what’s covered, here is the table of contents:

1. Genome assembly and annotation…………………………………………………………… 2

1.1 Downloading E. coli sequences for assembly…………………………………………….. 2

1.2 Examining quality of reads (FastQC)………………………………………………………… 2

1.3 Velvet – assembling reads into contigs………………………………………………………. 4

1.3.1 Using VelvetOptimiser to optimise de novo assembly with Velvet………….. 6

1.4 Ordering contigs against a reference using Mauve………………………………………. 7

1.4.1 Viewing the ordered contigs (Mauve)………………………………………………… 10

1.4.2 Viewing the ordered contigs (ACT)……………………………………………………. 13

1.5 Mauve Assembly Metrics – Statistical View of the Contigs………………………… 15

1.6 Annotation with RAST……………………………………………………………………………. 15

1.6.1 Alternatives to RAST………………………………………………………………………. 19

2. Comparative genome analysis……………………………………………………………….. 20

2.1 Downloading E. coli genome sequences for comparative analysis………………. 20

2.2 Mauve – for multiple genome alignment……………………………………………………. 21

2.3 ACT – for detailed pairwise genome comparisons……………………………………… 24

2.3.1 Generating comparison files for ACT…………………………………………………. 24

2.3.2 Viewing genome comparisons in ACT……………………………………………….. 27

2.4 BRIG – Visualizing reference-based comparisons of multiple sequences……… 29

3. Typing and specialist tools……………………………………………………………………. 34

3.1 PHAST – for identification of phage sequences…………………………………………. 34

3.2 ResFinder – for identification of resistance gene sequences………………………… 34

3.3 Multilocus sequence typing…………………………………………………………………….. 34

3.4 PATRIC – online genome comparison tool………………………………………………… 34

http://pimpmyphd.blogspot.com.au/2012/03/how-not-to-miss-almost-any-article-in.html

Unfortunately this seems to be the only post on the brilliantly named Pimp My PhD blog.

I think this is a great idea, and as founding editor Phil Bourne points out, are a far better option for both readers and authors than the ‘traditional’ science books made up of contributed chapters, which are hard to access, expensive and rarely cited.

Of particular interest to us in the microbial world is Chapter 12: Human Microbiome Analysis by Xochitl C. Morgan, Curtis Huttenhower from Harvard.

Being a book-chapter-style document, it includes some really useful ‘extras’ including questions to get you thinking about what you’ve learnt from the article (and answers in the supplementary), a useful glossary and pointers for further reading.

Because it is PLoS, I can show you exactly what is in it:

1. Introduction
2. A Brief History of Microbiome Studies
3. Taxonomic Diversity
4. Shotgun Sequencing and Metagenomics
5. Computational Functional Metagenomics
6. Host Interactions and Interventions
7. Summary
8. Exercises
Supporting Information
Acknowledgments
References

Figures

Figure 1. Bioinformatic methods for functional metagenomics.
Studies that aim to define the composition and function of uncultured microbial communities are often referred to collectively as “metagenomic,” although this refers more specifically to particular sequencing-based assays. First, community DNA is extracted from a sample, typically uncultured, containing multiple microbial members. The bacterial taxa present in the community are most frequently defined by amplifying the 16S rRNA gene and sequencing it. Highly similar sequences are grouped into Operational Taxonomic Units (OTUs), which can be compared to 16S databases such as Silva, Green Genes, and RDP to identify them as precisely as possible. The community can be described in terms of which OTUs are present, their relative abundance, and/or their phylogenetic relationships. An alternate method of identifying community taxa is to directly metagenomically sequence community DNA and compare it to reference genomes or gene catalogs. This is more expensive but provides improved taxonomic resolution and allows observation of single nucleotide polymorphisms (SNPs) and other variant sequences. The functional capabilities of the community can also be determined by comparing the sequences to functional databases (e.g. KEGG or SEED). This allows the community to be described as relative abundances of its genes and pathways. 
doi:10.1371/journal.pcbi.1002808.g001

Figure 2. Ecological representations of microbial communities: collector’s curves, alpha, and beta diversity.
These examples describe the A) sequence counts and B) relative abundances of six taxa (A, B, C, D, E, and F) detected in three samples. C) A collector’s curve, typically generated using a richness estimator such as Chao1 or ACE, approximates the relationship between the number of sequences drawn from each sample and the number of taxa expected to be present based on detected abundances. D) Alpha diversity captures both the organismal richness of a sample and the evenness of the organisms’ abundance distribution. Here, alpha diversity is defined by the Shannon index, where pi is the relative abundance of taxon i, although many other alpha diversity indices may be employed. E) Beta diversity represents the similarity (or difference) in organismal composition between samples. In this example, it can be simplistically defined by the equation , where n1 and n2 are the number of taxa in samples 1 and 2, respectively, and c is the number of shared taxa, but again many metrics such as Bray-Curtis or UniFrac are commonly employed.
doi:10.1371/journal.pcbi.1002808.g002

Happy reading!

Sometimes I think this is just me being a map-o-phile, but when we didn’t include a map in our recent paper on the dissemination of Shigella sonnei, the maps ended up being created anyway by the authors of two commentary articles! (Commentaries here and here.)

So, I often find I need to indicate on a global map which countries we have sampled in a study. Here are two ways to do it:

(1) GeoChart Map Generator

This is a web tool where you just click on the name of the countries you want to colour and they are filled in on the map. The advantage is it’s quick and easy, and will produce an image good enough to take a screenshot for insertion into a PowerPoint or web page. Disadvantage is the resolution isn’t really good enough for printing out and definitely not high enough resolution for a figure in a paper.

Here’s an example:

Similar apps are available on other sites, including http://www.ammap.com/visited_countries/.

(2) Edit a SVG map in Adobe Illustrator or a similar graphics editor. You can download suitable maps from Wikimedia Commons - http://commons.wikimedia.org/wiki/Category:Blank_SVG_maps_of_the_world

This will give you a publication-quality figure, which you can save straight to PDF. To select the right countries to colour in, you’ll need to know where they are on the map (!). It can be handy to use one of the web tools first to help locate all the countries if your geography isn’t great.

Here’s an example, showing the countries covered in the Shigella sonnei study:

For some ideas on combining trees with maps, ie phylogeography, see this site for building tree maps for BEAST analyses using SPREAD, or try GenGIS.

Part I: Eurosurveillance, Volume 18, Issue 3, 17 January 2013

Download whole issue as PDF: http://www.eurosurveillance.org/images/dynamic/EE/V18N03/V18N03.pdf

Part II: Eurosurveillance, Volume 18, Issue 4, 24 January 2013

My only gripe is that only 5/11 (45%) articles in the issue are open access

Luckily the best article is among the open access ones – a fantastic review of metagenomic studies, from experimental design and sampling right through to data analysis and submission to public archives, written by Hanno Teeling and Frank Glöckner from the Max Planck Institute for Marine Microbiology. Full text is online here or as a PDF.

Most of the other articles cover new tools for churning through your metagenomic sequence data and figuring out what is in there in terms of function and/or taxonomy. There are many approaches to this and several tools already out there including the very beautiful MG-RAST and Real Time Metagenomics. I have also been tinkering with these to explore the “pan-genomes” of various bacterial species where we have hundreds of genomes available… not quite what they were intended for but it seems to work quite nicely, and gives you some great insights into the spectrum of accessory genes that are flowing through various bacterial populations.

It looks for possible prophages in your bacterial genomes, and makes such beautiful pictures of the results, like this summary of the five phage it found in a new Salmonella genome:

It also draws nice circular diagrams to show you where the phage are located, like this:

And it will even show you a nicely annotated figure of indidual phage it found, using an interactive Flash viewer:

My only gripe is that unlike some of the more visualization-challenged phage finders, PHAST doesn’t output actual annotation files, like GenBank or GFF or even a  simple text table that would be straightforward to convert into GenBank… the format in which it prints out the actual information on where each phage is located in your sequence seems to be a home-grown text format that is not easy to parse with existing tools.

Oh well, I suppose I will have to write a little script to turn PHAST’s phage hunt results into a proper annotation… unless someone else has already done this?

However, it is obviously useful to be able to extract MLST info from genome assemblies too. For example, many finished or WGS genome sequences in NCBI do not have ST information attached to them, or it is hard to find. Also, for 454 and perhaps Ion Torrent data, it can be easier to deal with homopolymer issues at the assembly level by using newbler/gsAssembler and then working with contigs.

There is a web service available that is designed to do this, i.e. you can upload your genomes and choose a MLST scheme, and it will return the ST. It is described in this paper and available at this URL. However, unfortunately I have never been able to get the website to load in any of my web browsers, so I’ve not been able to try it. Also, it is a pain to have to upload large amounts of data over the web, and this becomes completely infeasible when dealing with lots of genomes, so instead I use a simple script to extract MLST info via blast, which runs locally on my laptop or cluster.

The script and a short readme containing usage instructions are available at: http://sourceforge.net/projects/srst/files/mlstBLAST/

I’m sure many people have written in-house scripts for this same task, but a few people have asked for mine recently and I figure it might save some others reinventing the wheel. The script simply uses BioPython to run a set of nucleotide blast searches in order to assign STs to genome assemblies. The inputs are just the latest set of allele sequences and profiles for the MLST scheme, and whatever genome assemblies you wish to determine STs for. The script will then determine the ST for each input genome, and if an exact match can’t be found, it will try to figure out the closest matching alleles and ST.

Happy sequence typing!