Mapping tutorial for Porecamp 2016
In this tutorial we will explore the types of data that the MinION produces, and try to look at the error mode by visual inspection of alignments.
WARNING: You might get strange errors when copying and pasting commands from this file into a terminal window if the text contains double-quote characters. In these situations, please type in the double-quotes yourself.
We’ll be using one sample sequenced for the Nick and Josh’s Ebola sequencing project.
The reads are already on the PoreCamp2016 server in /data/raw/hist/Ebola_R7 (downloaded from the ENA project PRJEB10571 sample ERR1014225).
You will be putting files into a sub-directory of your home directory.
cd mkdir MappingTute cd MappingTute
Extract the data using poretools
poretools is a tool for extracting and interrogating nanopore data published by Nick Loman and Aaron Quinlan.
First, we’ll extract the 2D pass reads in FASTA format:
poretools fasta --type 2D /data/raw/hist/Ebola_R7/reads/pass > Ebola2D.fasta
How many reads do we have?
grep ">" Ebola2D.fasta | wc -l
Download the reference genome
We can use wget to download a file on the web directory to our server
If you are running in X2Go run:
And then create the bwa index file required to run bwa mem later
bwa index EM_079517.fasta
Map the reads
And now we actually map the reads, convert the SAM output to BAM format and then sort it by mapping coordinate (rather than read name) and save it as Ebola2D.sorted.bam and create the SAM index file required to run other samtools subtools later.
bwa mem -x ont2d EM_079517.fasta Ebola2D.fasta | samtools view -bS - | samtools sort -o Ebola2D.sorted.bam -
samtools index Ebola2D.sorted.bam
Basic QC of the data
As a first QC of the aligned reads, we can run samtools stats
samtools stats Ebola2D.sorted.bam > Ebola2D.stats.txt head -n 40 Ebola2D.stats.txt
- How many reads were mapped?
- What was the average length of the reads?
We can also plot the read depth across the reference genome by using the output of samtools stats and then plotting in Rstudio
grep "^COV" Ebola2D.stats.txt > Ebola2D.coverage.txt
First, in a web browser, open 184.108.40.206:8773 then type in your group username and password. Then Rstudio should open for you and you can type the following:
library(ggplot2) cov=read.table("/path/to/your/Ebola2D.coverage.txt", sep="\t") cov[1,] ggplot(cov, aes(x=V3, y=V4)) + geom_bar(stat='identity') + xlab('coverage') + ylab('count')
You could also do something similar using the output of samtools depth if you have time later.
Consolidating your knowledge
Now, repeat this process from the beginning, but do it for a different dataset, choose from:
- All 1D pass reads (hint: –type fwd,rev)
- All pass forward reads (hint: –type fwd)
- All pass reverse reads (hint: –type rev)
- All 2D fail reads (hint: –type 2D, use the fail directory)
1D reads only! Ensure you use a different file name, e.g. Ebola1D.fasta
- How does the number of reads change?
- How does the mapping frequency change?
Now, let’s download the BAM file and inspect the alignment. My favoured tool for this is Tablet. It requires Java.
You need to copy the files from the server to your laptop using a GUI interface like WinSCP or filezilla or use the scp command in a terminal window or PuTTY by typing the following on your laptop:
cd /path/to/your/workingdirectory scp groupX@220.127.116.11:/path/to/your/something.bam .
You need to load the following two files into Tablet:
alignment file: Ebola2D.sorted.bam reference file: EM_079517.fasta
Inspect the alignment.
- Did the alignment confirm your earlier suspicions about how the sample was prepared?
- What are the pros and cons of this approach?
- Which regions might you be suspicious of?
Have a look at the error profile. Are some parts of the genome better than others? Can you correlate this with the sequence?
The Ebola virus mutation rate is in the order of 1.2 x 10^-3 mutations/site/year. The genome size is 19000 bases long. This sample was collected about a year after the reference genome. Approximately how many SNPs do you expect to see?
Call SNPs - by eye!
- Make a list of SNPs - which ones are hard to assess?
Variant calling with nanopolish
Calling variants with nanopolish relies on squiggle data to generate the best consensus and gives a nicer result.
To call variants, there are three steps:
- align the reads with BWA (or another aligner, such as marginAlign, or LAST)
- align the events with nanopolish eventalign
- call a VCF with nanopolish variants
Copy the model files into your current directory from: /data2/models/ into your current directory.
cp /data2/models/* .
We’ve already aligned the reads (output file from BWA was Ebola2D.sorted.bam)
nanopolish-r7 eventalign --reads Ebola2D.fasta -b Ebola2D.sorted.bam -g EM_079517.fasta --sam | samtools view -bS - | samtools sort -o Ebola2D.eventalign.bam -
We need to index the new BAM file that nanopolish eventalign produced:
samtools index Ebola2D.eventalign.bam
And now we need to get the variants in VCF format:
nanopolish-r7 variants --progress -t 1 --reads Ebola2D.fasta -o Ebola2D.eventalign.vcf -b Ebola2D.sorted.bam -e Ebola2D.eventalign.bam -g EM_079517.fasta -vv -w EM_079517:0-20000 --snp
It is actually possible to use different models with nanopolish variants specifying the model filenames –models-fofn offset_models.fofn. In this case we swap the original 5-mer model for a 6-mer model.
Compare this list with the list of variants that you already eyeballed. How do they compare?
Did nanopolish spot things that you didn’t?
Did nanopolish get anything wrong? Could you figure out a way of filtering the VCF to remove these errors?
To get the consensus sequence from the reference, vcf and bam file:
/home/ubuntu/scripts/margin_cons.py EM_079517.fasta Ebola2D.eventalign.vcf Ebola2D.sorted.bam > Ebola2D.eventalign.consensus.fasta 2> Ebola2D.eventalign.variants.txt
SNP calling with 6-mer model
nanopolish-r7 variants --progress -t 1 --reads Ebola2D.fasta -o Ebola2D.6mer.vcf -b Ebola2D.sorted.bam -e Ebola2D.eventalign.bam -g EM_079517.fasta -vv -w "EM_079517:0-20000" --snp --models-fofn offset_models.fofn
How does the new VCF Ebola2D.6mer.vcf look compared with the old one?
This tutorial was tested with the following software versions:
- samtools version 1.3.1
- bwa version 0.7.15-r1140