1. Introduction of bwa

Objective:
After quality control, BWA MEM compared the quality controled data to the reference genome.
Algorithm:
BWA is a fast comparison tool based on BWT. It consists of three algorithms. The three algorithms are BWA Backtrack, BWA SW, and BWA MEM. Among them, BWA MEM is the latest, which is faster, more accurate, and more suitable for human weight data analysis.
Installation:

conda install -c bioconda bwa

2. Bwa process :(see help file for details)

Index building
# Establish AN FM-Index for large genomes

bwa index -a bwtsw $reference

Establish index for small genome with fast speed and large memory consumption

bwa index -a is the ref. fasta bwa index ./2019-nCoV.fasta

3. Single two-terminal data comparison :(the input data is trim after)

bwa mem -t 8 ./bwa_index/2019-nCoV.fasta out.R1.fq.gz out.R2.fq.gz > 2nd.sam

4. Batch double-end data comparison:

INDEX=./bwa_index/2019-nCoV.fasta for i in $(ls *_) Cat/holds the trim fastq file |while read id do arr=($id) sample=${arr[0]} fq1=${arr[1]} fq2=${arr[2]} echo $sample $fq1 $fq2 bwa mem -t 20 $INDEX /home/kelly/wesproject/4_clean/wes/$fq1 /home/kelly/wesproject/4_clean/wes/$fq2 |samtools sort -@ 20 -o $sample.bam done

5. The result:

Get the Samtools input Sam file for the next step
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