Short Read Assembly with Velvet

Warning

These documents are not maintained and their instructions may be out of date. However the GED Lab does maintain the khmer protocols which may cover similar topics. See also the installation instructions for the current version of the khmer project.

Author:Jason Pell
Date:June 7, 2011
Last Updated:June 9, 2011

For this tutorial, we will be using the short read de novo assembler Velvet to assemble a bacterial genome. However, there are plenty of other assemblers out there (e.g. ABySS, ALLPATHS 2, SOAPdenovo, etc.) that may be more appropriate for your particular dataset, and we can help you get them installed if you are interested.

Getting Started

Start or log in to an instance on Amazon EC2. You will need to have Dropbox set up (see Installing dropbox on your EC2 machine) and the data directory snapshot mounted (see ‘Getting the data’ at Checking read quality with FastQC).

Go to your /mnt directory where there is more free space:

%% cd /mnt

Next, we need to obtain some different files. To obtain Velvet, use curl:

%% curl -O http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.1.04.tgz

Now, we’ll copy our datasets to /mnt and uncompress them:

%% cp /data/ecoli/SRR001666_*.fastq.gz /mnt
%% gunzip SRR001666_*.fastq.gz

This dataset is an Illumina run of E. coli with 36bp paired-end reads and a 500bp insert size. A similar dataset with an insert size of 200bp is available under accession number SRR001665 from NCBI or EBI if you are interested in trying to assemble them together (though it doesn’t improve the quality of the assembly very much).

We will also need some packages installed:

%% apt-get install make

Installing Velvet

Uncompress the tarballs and cd into the Velvet directory:

%% tar xvzf velvet_1.1.04.tgz
%% cd velvet_1.1.04

Once you are in the Velvet directory, run the following to install:

%% make 'MAXKMERLENGTH=49'

This command will compile the package. The MAXKMERLENGTH parameter is created as a tradeoff between memory efficiency and flexibility with the ‘k’ parameter. We have it set to be more than enough for our purposes, but you may need to set MAXKMERLENGTH higher depending on your dataset.

You may get an error that some of the documentation was unable to build, but that’s ok.

We will now “install” Velvet onto your instance:

%% cp velveth /usr/bin
%% cp velvetg /usr/bin

Running Velvet

Before we actually run Velvet, we need to “interleave” the two FASTQ files since they are one paired-end library:

%% cd ..
%% velvet_1.1.04/shuffleSequences_fastq.pl SRR001666_1.fastq SRR001666_2.fastq reads.fastq

Assembling with Velvet is a two-step process:

%% mkdir k31
%% velveth k31 31 -shortPaired -fastq reads.fastq
%% velvetg k31 -ins_length 500

The 31 is the value that we are selecting for the K parameter. This means that we are using 31-mers to look for overlaps between the reads. There is a tradeoff between “sensitivity” and “specificity” that we will discuss later on in the tutorial.

Evaluating Assemblies

Assessing the quality of a de novo assembly where there is no good reference is still an open problem. However, there are many statistics that can be useful in comparing assemblies to one another. We have a Python script that provides many of these statistics; it’s in the ngs-course scripts, under ‘ngs-course/assembly/assemstats3.py’.

Before you can run it, you must install screed, so we’ll run the following in the home directory:

%% git clone git://github.com/ctb/screed.git
%% cd screed
%% python setup.py install

Screed is a software package that was developed to easily parse and manipulate a large amount of short read sequences. Once the reads are indexed, you can very quickly retrieve any sequence you need by name. However, the assembly statistics Python script just uses the provided FASTA parser.

To obtain statistics on the file you just generated, run:

%% cd /mnt
%% python ~/Dropbox/ngs-scripts/assembly/assemstats3.py 0 k*/contigs.fa

Other Stuff To Try

The optimal value for k depends greatly on the dataset. A lower value for k has greater sensitivity, but can produce more false overlaps. However, it is the best option when you don’t have high coverage. On the other hand, a high value for k will have a more accurate assembly and longer contigs, but you are likely to miss a lot of potential read overlaps, which means you need higher coverage to make up for the difference.

Try varying the value for k by creating a new directory for each value that you would like to test. With Velvet, you can only choose odd number k-mers. Furthermore, you must choose a k that is smaller than the read length, so in this case k < 36. After you have created all of your assemblies, run:

%% python ~/Dropbox/ngs-scripts/assembly/assemstats3.py 0 k*/contigs.fa

again to see how the assemblies compare to each other. If you generate a lot of assemblies, you can copy and paste the output to a text file and import it into Excel as a space-delimited file.

We have another script for you to try called extract-long-sequences.fa. This script acts as a simple filter to get rid of sequences smaller than a certain length. For example, if you have a file named contigs.fa and you want only contigs of length 200 or greater, you can run:

%% python ~/Dropbox/ngs-scripts/assembly/extract-long-sequences.py 200 contigs.fa > out.fa

Finally, if you have your own dataset, you can try to assemble it on your EC2 system. However, you may want to check memory usage with the top command in order to ensure that you are not using too much memory. If the Velvet memory usage is over 90%, you may be using virtual memory, which means the assembly will take much longer than necessary.


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