bwa
bwa is a software that aligns sequences to a reference genome. The commonly used algorithm is BWA-MEM.
The BWA-MEM algorithm is more effective than the BWA-backtrack algorithm when comparing sequences with a length of 70-100bp. Normally, the BWA-MEM algorithm is selected.
bwa cheap
git clone https://github.com/lh3/bwa.git
cd bwa
make
make install
Compilation failed, other sources of yum are needed
use bwa
(1) bwa creates an index:
method one:
bwa index mm10.fasta
Method Two:
bwa index mm10.fasta -p genme
Method three:
bwa index -a bwtsw ref.fasta #对于大基因组建立FM-Index
Method four:
bwa index -a is ref.fasta #对小基因组建立index，速度快，内存消耗大
(2) bwa sequence alignment, create sam file
bwa mem -t 4 genome F2-19.1.fastq F2-19.2.fastq > F2-19.mem.sam