Quality control by mapping(2)¶
Map the data to the Wuhan reference:
minimap2 -a -t 14 ~/workdir/wuhan.fasta ~/workdir/assembly/assembly_wgs/assembly.contigs.fasta | samtools view -b - | samtools sort - > ~/workdir/mappings/assembly_wgs_vs_wuhan.sorted.bam
Create the index:
samtools index ~/workdir/mappings/assembly_wgs_vs_wuhan.sorted.bam
Load GenomeView with:
java -jar ~/genomeview-N42.jar
Load the wuhan reference and the mapping and look at the data - is it more equally distributed?
In the next step, we perform the assembly with canu and the WGS dataset.References¶
Minimap2 https://github.com/lh3/minimap2
samtools http://www.htslib.org