Get coverage stats for a LOT of reference sequences

Sometimes we need to map reads to a multi-fasta reference with lots of sequences, e.g. to screen for large sets of genes or plasmids. The mapping works fine, but it can be tricksy to get alignment statistics (such as % of reads mapped) broken down by reference sequence, using common tools like Samtools, Bamtools or Bamstats.

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.

Bacterial genomics tutorial

This is a shameless plug for an article and accompanying tutorial I’ve just published together with David Edwards, my excellent MSc Bioinformatics student from the University of Melbourne. It’s currently available as a PDF pre-pub from BMC Microbial Informatics and Experimentation, but the web version will be available soon. The accompanying tutorial is available here.

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 ]

Figure1_Velvet 

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 ]

Figure2_ACT

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 ]

Fig3_Mauve

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 ]

Fig4_BRIG

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

Human Microbiome Analysis – PLoS Computational Biology eBook

PLoS has made it’s first foray into ‘book’ publishing, with it’s new collection from PLOS Computational Biology called Translational Bioinformatics.

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:

Abstract

Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.

Citation: Morgan XC, Huttenhower C (2012) Chapter 12: Human Microbiome Analysis. PLoS Comput Biol 8(12): e1002808. doi:10.1371/journal.pcbi.1002808

What to Learn in This Chapter

  • An overview of the analysis of microbial communities
  • Understanding the human microbiome from phylogenetic and functional perspectives
  • Methods and tools for calculating taxonomic and phylogenetic diversity
  • Metagenomic assembly and pathway analysis
  • The impact of the microbiome on its host

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!

Colouring in country maps

If there’s one thing I love more than a good tree it’s a good map. (And how wonderful it is when they combine!) In genomic epidemiology, maps are often super important for visualising where bacterial genomic data has come from and how bugs are moving about.

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:

mapgenerator

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:

Shigella_Map_countriesRed

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.

Eurosurveillance special issues on molecular epidemiology of human pathogens

January 2013 heralds 2 special issues of Eurosurveillance with some great articles, including some visions of how whole genome bacterial sequencing does and will fit in with public health labs. All articles are free and open access. The tables of contents are below, note you can download the whole first issue as a single PDF.

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

Table of Contents
MISCELLANEOUS
by Eurosurveillance editorial team
RESEARCH ARTICLES
by R Rykkvin, A Kilander, SG Dudman, O Hungnes

by SA Chisholm, M Unemo, N Quaye, E Johansson, MJ Cole, CA Ison, MJ Van de Laar

by MM Fitzgibbon, N Gibbons, E Roycroft, S Jackson, J O’Donnell, D O’Flanagan, TR Rogers
SURVEILLANCE AND OUTBREAK REPORTS
by F de Marval, B Gottstein, M Weber, B Wicht
PERSPECTIVES
by P Muellner, E Pleydell, R Pirie, MG Baker, D Campbell, PE Carter, NP French
NEWS
by I van Walle

by Eurosurveillance editorial team

by Eurosurveillance editorial team



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

EDITORIALS
by MJ Struelens, S Brisse
EUROROUNDUPS
by BA Lindstedt, M Torpdahl, G Vergnaud, S Le Hello, FX Weill, E Tietze, B Malorny, DM Prendergast, E Ní Ghallchóir, RF Lista, LM Schouls, R Söderlund, S Börjesson, S Åkerström
REVIEW ARTICLES
by AJ Sabat, A Budimir, D Nashev, R Sá-Leão, JM van Dijl, F Laurent, H Grundmann, AW Friedrich, on behalf of the ESCMID Study Group of Epidemiological Markers (ESGEM)

by JA Carriço, AJ Sabat, AW Friedrich, M Ramirez, on behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM)

by KA Jolley, MC Maiden
SURVEILLANCE AND OUTBREAK REPORTS
by HG Niesters, JW Rossen, H van der Avoort, D Baas, K Benschop, EC Claas, A Kroneman, N van Maarseveen, S Pas, W van Pelt, JC Rahamat-Langendoen, R Schuurman, H Vennema, L Verhoef, K Wolthers, M Koopmans
RESEARCH ARTICLES
by CW Knetsch, TD Lawley, MP Hensgens, J Corver, MW Wilcox, EJ Kuijper
PERSPECTIVES
by RV Goering, R Köck, H Grundmann, G Werner, AW Friedrich, on behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM)

by B Rump, C Cornelis, F Woonink, M Verweij

Metagenomics analysis special issue in Briefings in Bioinformatics

This month’s Briefings in Bioinformatics issue is devoted to “Bioinformatics approaches and tools for metagenomics analysis“. Yay! I love special issues, especially when they bring together lots of tools to tackle a set of similar problems.

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.