DNA was prepared according to the Damaged library improvement protocol
with size selection using BluePippin 0.75% DF Marker S1 high-pass
6-10kb v3 protocol with BPstart of 6kb.
Libraries were generated with the SQK-LSK108 Ligation Sequencing Kit
1D (R9.4) and sequenced using SpotON R9.4 flowcells on a MinION Mk 1B.
In our analyses we declare PASS reads to be at least 1 k base in length and have and average quality of 14 or more.
Reads were mapped to hs37d5lam.fasta including lambda phage control sequences using "bwa mem" with the following options: -x ont2d -t 12 -R "@RG\tID:1\tSM:NA12878" -M.
Reads were mapped per flow-cell and then merged using samtools merge to produce the final output, comprising bam and bam index (.bai) files. PASS and FAIL reads are provided in separate files.
Oxford Nanopore MinION data from Wellcome Trust Centre for Human Genetics
logistics
/share/PI/mrivas/data/WTCHG/data description from README
-x ont2d -t 12 -R "@RG\tID:1\tSM:NA12878" -M.samtools mergeto produce the final output, comprising bam and bam index (.bai) files. PASS and FAIL reads are provided in separate files.