Genome_assembly

#!/bin/bash
a=ERR4627396.sra_1.fastq
b=ERR4627396.sra_2.fastq
d=ERR4627396.skesa.fa

fastp -i $a -I $b -o ERR4627396.sra_1.fq -O ERR4627396.sra_2.fq 

skesa --fastq ERR4627396.sra_1.fq,ERR4627396.sra_2.fq  > $d

bwa index ERR4627396.skesa.fa

bwa mem ERR4627396.skesa.fa $a $b > ERR4627396.sam

samtools sort ERR4627396.sam -o ERR4627396_sort.bam

qualimap bamqc -bam ERR4627396_sort.bam -outfile ERR4627396_qualimap_results