Prediction pipeline

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  1. Whole reads were mapped against reference genome
  2. Both unmapped reads retrieve using following command
samtools view –hb –f 12 –F 256 input.bam > output.bam
  1. Make fastq file in bam file using bam2fastq
  2. Denovo assemble of both unmapped reads using AbySS with k-mer = 51 and q-value = 20
  3. Denovo assemble of whole sequencing reads using AbySS with k-mer = 51 and q-vale = 20
  4. BLASTN between contigs derived from whole sequencing reads and those derived from both unmapped reads which are longer than 2k with e-value threshold, 1e-100