Using enadownloader to download fastqs from the ENA

I wanted to download fastq files for a long list of SRR accessions from the ENA today.

I realised I could use the enadownloader tool that I previously wrote a blogpost about a while ago.

Here's how I used enadownloader to download the fastq files, on the Sanger compute farm:

First I checked which is the latest version of the enadownloader tool on the farm:

% module avail -t | grep -i ena 

Then I loaded the module:

% module load enadownloader/v2.3.5-4ac05c8f

Then I made a file of all the SRR accessions, called 'srr_accessions' like this:

SRR31024208
SRR31024304
SRR31024307

...

Then I made an output directory 'srr_accessions_fastqs' to put the fastqs in:

% mkdir srr_accessions_fastqs 

Then I used enadownloader to download the fastqs for all these accessions:

% enadownloader -t run -i srr_accessions -d -o srr_accessions_fastqs

where -t run means the type of data is sequence runs, -i srr_accessions means the input file is srr_accesions, -d means that I want to download data, -o srr_accessions_fastqs means the output directory is srr_accessions_fastqs.

Nice and easy!

 

 

Making assemblies for Oxford Nanopore sequence data using Dragonflye

I've been making genome assemblies for some Oxford Nanopore Technology (ONT) sequencing data using the Dragonflye package by Robert A. Petit III. 

It was super easy to run!

Here's how I ran it on the Sanger compute farm:

First I found the version of Dragonflye on the farm:

% module avail -t | grep -i dragon

Then I loaded it:

% module load dragonflye/1.2.1

Then I assembled sequence reads for a Vibrio cholerae isolate into an assembly using Dragonflye: 

%  dragonflye --reads SRR31024125_1.fastq.gz --outdir SRR31024125_1.fastq_dragonflye --gsize 4000000

where  SRR31024125_1.fastq.gz was my input fastq file of ONT reads,

SRR31024125_1.fastq_dragonflye was the name that I wanted to give to the output directory,

 --gsize 4000000 specifies that the Vibrio cholerae genome is about 4.0 Mbase.

The output file was called SRR31024125_1.fastq_dragonflye/contigs.fa.  

It took about 20 minutes to make the assembly. The input file of ONT reads was about 93 Megabytes (SRR31024125_1.fastq.gz).