FastQC is a Java-based software, usually in a linux environment line run with the command, it can quickly multithreading to assess the quality of sequencing data (at Quality Control)
zcat tmp.fq.gz | head -10000> tmp. fq: view the compressed file to take the first 10,000 lines into tmp.fq file.
cat tmp.fq | paste ---- | cut -f 2 | cut -c 1 | sort | uniq -c: View tmp.fq file, four lines become one line, whichever is longer cutting whichever of the second column a character, sort, remove duplicates and count the number of repetitions.
Use bwa comparison:
tmp.sam bwa mem prefix of the index tmp.fq>: to generate more than .sam file
bwa mem prefix of the index tmp.fq> tmp.sam: compare files generated .bwa.log
.Sam to convert files into .bam file:
samtools View -bs tmp.sam> tmp.bam
View .bam file:
samtools View -h tmp.bam (-h: View of the head)
.Bam sort of file:
samtools the Sort tmp.bam> tmp.sorted.bam
Find variation ():
samtools mpileup -ugf hg38.fa .bam | bcftools Call -vmo z -a rmdup.bcftools.vcf.gz
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