Mapping the polished assembly to the reference
To evaluate the polishing of the first assembly we will now map the polished contigs to the reference genome using LAST. We will re-use the index we generated earlier for the reference.
Now that we have an index, we can map the assembly to the reference, convert the output to SAM and finally to BAM format:
cd ~/workdir/pilon
minimap2 -a data/Reference.fna pilon/pilon_round4.fasta > pilon4toref.sam
samtools view -b pilon4toref.sam > pilon4toref.bam
samtools sort pilon4toref.bam > pilon4toref.sorted.bam
samtools index pilon4toref.sorted.bam
To look at the BAM file use:
samtools view pilon4toref.bam | less
We will use a genome browser to look at the mappings. Start IGV:
igv
Now let’s look at the mapped contigs:
Load the reference genome into IGV. Use the menu
Genomes->Load Genome from File...Load the BAM file into IGV. Use menu
File->Load from File...
References
minimap2 https://github.com/lh3/minimap2
samtools http://www.htslib.org