Mapping PacBio and MinION reads using bwa
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bwa index -a bwtsw /data/assembly/NC_000913_K12_MG1655.fasta
bwa mem -t 2 -x ont2d /data/assembly/NC_000913_K12_MG1655.fasta /data/MAP006-1_2D_pass.fastq | samtools view -buS - | samtools sort - -o map_ONT.sorted.bam
samtools index map_ONT.sorted.bam
bwa mem -t 2 -x pacbio /data/assembly/NC_000913_K12_MG1655.fasta /data/assembly/pacbio/Analysis_Results/m141013_011508_filtered_subreads_30x.fastq | samtools view -buS - | samtools sort - -o map_PacBio.sorted.bam
samtools index map_PacBio.sorted.bam