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- #!/bin/bash
-
- mkdir results
-
- # Question 1
- soft/bowtie2 --end-to-end --fast -x databases/all_genome.fasta -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -S results/alignment.sam
-
- # Question 2
-
- # a
- samtools view -b results/alignment.sam
-
- # b
- samtools sort -@ 4 results/alignment.bam -o results/alignment.sorted.bam
-
- # c
- samtools index results/alignment.sorted.bam
-
- # d
- samtools idxstats -@ 4 results/alignment.sorted.bam > results/alignment.idx
-
- # f
- grep ">" databases/all_genome.fasta|cut -f 2 -d ">" > results/association.tsv
-
- # Question 3
-
- soft/megahit --k-list 21 --mem-flag 0 -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -o contigs
-
- # Question 4
-
- soft/prodigal -i contigs/final.contigs.fa -f fasta > genes.fna
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