This bash script design for reference based chloroplast genome assembly
written by Dr. Manosh Kumar Biswas @UOL, UK 26April 2022
WorkFlow 1. Download Ensete NGS raw read from SRA database of NCBI using SRA id [Make SRA data list in text file]
2. Check Quality then Clean and trim SRA reads
3. Map clean R1 and R2 SRA reads in references CP genome [eg. Banana or ensete ]
4. Extract consesus sequences assembly
5. Functional Annotation CP genes
1. sratoolkit [fastq-dump.3.0.0]
2. fastqc, multiQC, Trimmomatic
3. BOWTIE2, samtools [view, bam2fq]