Mapping PacBio and MinION reads using bwa
¶
To run reapr
on assemblies, we need a bam
file. We need to specify some
extra options when running bwa
on pacbio og minion data.
Index reference genome¶
We are mapping the reads to their assemblies. To do that, we need an index:
bwa index -a bwtsw ASSEMBLY.FASTA
Mapping MinION data¶
Run this command after indexing.
bwa mem -t 3 -x ont2d /path/to/ASSEMBLY.FASTA \
/share/inf-biox121/data/assembly/MAP006-1_2D_pass.fastq | \
samtools view -buS - | \
samtools sort - -o map_ONT.sorted.bam
samtools index map_ONT.sorted.bam
Mapping PacBio data¶
Run this command after indexing.
bwa mem -t 3 -x pacbio /path/to/ASSEMBLY.FASTA \
/share/inf-biox121/data/assembly/m141013_011508_filtered_subreads_30x.fastq | \
samtools view -buS - | samtools sort - -o map_PacBio.sorted.bam
samtools index map_PacBio.sorted.bam