I'm a starting my analysis on nanopore whole genome sequencing. I start my analysis from this popular Github.
The sample I downloaded was WGS for NA12878, so I would assume it's alignment to GRCh38 shouldn't be that bad.
But ... I'm getting lot's of insertions...
I'm not sure it was caused by the sequencing platform, the MiniMap aligner or my bugs.
I supply all my commands, starting from sample download.
wget https://s3.amazonaws.com/nanopore-human-wgs/rel5-guppy-0.3.0-chunk10k.fastq.gz gunzip rel5-guppy-0.3.0-chunk10k.fastq.gz wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa minimap2 -d GRCh38_full_analysis_set_plus_decoy_hla.fa.index GRCh38_full_analysis_set_plus_decoy_hla.fa minimap2 -ax map-ont -t 20 GRCh38_full_analysis_set_plus_decoy_hla.fa.index rel5-guppy-0.3.0-chunk10k.fastq | samtools view -bS - | samtools sort -@ 5 > rel5-guppy-0.3.0-chunk10k.bam samtools index rel5-guppy-0.3.0-chunk10k.bam