1.Remapping

1. bwa index ref.fasta
   

2. bwa mem -k 19 -t 20 ref.fasta ${i}_1.fq.gz ${i}_2.fq.gz > ${i}.sam
   

3. samtools view -@ 30 -bS ${i}.sam > ${i}.bam
   

4. samtools view -b -F 12 ${i}.bam > ${i}.map.bam
   

5. samtools sort -@ 10 -n ${i}.map.bam -o ${i}.map.sorted.bam
   

6. bedtools bamtofastq -i ${i}.map.sorted.bam -fq ${i}_1.fq -fq2 ${i}_2.fq
   

7. spades.py -o ${i}/ -t 80 -1 ${i}.1.fq -2 ${i}.2.fq 1>spades.log 2>spades.er
   

---

20230303云南remapping

mkdir ./remapping

mkdir ./remapping/SARS-CoV-2

mkdir ./remapping/SARS-CoV-2/sam

mkdir ./remapping/SARS-CoV-2/bam

mkdir ./remapping/SARS-CoV-2/fq

mkdir ./remapping/SARS-CoV-2/assemble

cd remapping

在remapping/SARS-CoV-2目录下操作

1. #1.bwa.sh
   bwa index ref.fasta
   

2. #2.bam.sh  【24h】
   for i in `cat ../../result/metadata.txt`; do
   bwa mem -k 19 -t 40 /data1/zhangcg/db/ref_seq/SARS-CoV-2/ref/SARS-CoV-2_Wuhan-Hu-1.fasta ../../temp/qc/${i}_1.fastq ../../temp/qc/${i}_2.fastq > ./sam/${i}.sam; done
   

3. #3.sam.bam.sh	【24h】
   for i in `cat ../../result/metadata.txt`; do
   samtools view -@ 40 -bS ./sam/${i}.sam > ./bam/${i}.bam; done
   

4. #4.mpa.bam.sh	【1h】(24个)
   for i in `cat ../../result/metadata.txt`; do
   samtools view -@ 40 -b -F 12 ./bam/${i}.bam > ./bam/${i}.map.bam; done
   

5. #5.sort.bam.sh 【1min】
   for i in `cat ../../result/metadata.txt`; do
   samtools sort -@ 40 -n ./bam/${i}.map.bam -o ./bam/${i}.map.sorted.bam; done
   

6. #6.bam.fa.sh 【30s】
   for i in `cat ../../result/metadata.txt`; do
   bedtools bamtofastq -i ./bam/${i}.map.sorted.bam -fq  ./fq/${i}_1.fastq -fq2 ./fq/${i}_2.fastq; done
   

7. #7.assemble.sh 	
   for i in `cat ../../result/metadata.txt`; do
   megahit --continue --min-count 2 --min-contig-len 500 --k-min 27 --k-max 119 --k-step 10 -1 ./fq/${i}_1.fastq -2 ./fq/${i}_2.fastq -o ./assemble/${i} -t 40; done
   
   for i in `cat ../../result/metadata.txt`; do
   spades.py -o ./assemble/${i}/ -t 40 -1 ./fq/${i}_1.fastq -2 ./fq/${i}_2.fastq 1>spades.log 2>spades.er; done