Mapping of Illumina reads to assembly¶
We are mapping the Illumina reads our consensus sequence with BWA. BWA is a software package for mapping low-divergent sequences against a large reference genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate.
Mapping the Illumina data with bwa¶
First, we need to create an index on the consensus sequences:
bwa index ~/workdir/results_artic/barcode_01.consensus.fasta
Then, we run the actual mapping with:
bwa mem
and the following parameters:
Note: You don’t need to create a SAM file, when you pipe the results of bwa mem directly to samtools for SAM to BAM conversion and sorting:
<bwa command> | samtools view -b - | samtools sort - > ~/workdir/mappings/Illumina_vs_consensus_01.sorted.bam
The complete commandline for bwa mem is:
bwa mem -t 14 ~/workdir/results_artic/barcode_01.consensus.fasta ~/workdir/data_artic/Illumina_01/B0001_S1_L001_R1_001.fastq.gz ~/workdir/data_artic/Illumina_01/B0001_S1_L001_R2_001.fastq.gz > ~/workdir/mappings/Illumina_vs_consensus_01.sam
Then convert to BAM (if you didn’t created a sorted BAM file directly):
samtools view -b ~/workdir/mappings/Illumina_vs_consensus_01.sam | samtools sort - > ~/workdir/mappings/Illumina_vs_consensus_01.sorted.bam
And finally, no matter how you created the sorted BAM file, create an index on it:
samtools index ~/workdir/mappings/Illumina_vs_consensus_01.sorted.bam
Perform that step for the first (01) dataset only to save time. Do the other datasets later, when there is time left.