HPC应用&生命科学领域软件bwa详细安装使用教程

目录

1 项目发展

2 下载&测试

整体测试

---

1 项目发展

BWA是生物信息领域中常用的一款序列比对软件，目前针对BWA的优化主流手段是通过GPU来进行算法加速。bwa-gasal2项目就是基于gasal2的bwa,gasal2是一个基于GPU加速的基因比对库。 gasal2项目来自一篇论文GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data 项目的整体发展参考如下:

    graph LR
    C[nahmedraja/GASAL] -->
    A[nahmedraja/GASAL2] -->B[j-levy/GASAL2.1] -->
    D[j-levy/bwa-gasal2]

该项目已经完成了DCU适配.

2 下载&测试

https://cancon.hpccube.com:65024/1/main/DTK-23.04_hpcapps-202304/NFS3.2_CentOS7.6

注意使用与安装包相同的DTK-23.04

整体测试

./bwa-gasal2 index data/hg19.fa
#测试采用双端测序
./bwa-gasal2 gase_aln -t 12 -l 150 -e 3 data/hg19.fa data/SRR949537_1.fastq data/SRR949537_2.fastq > data/res_bwa_gasal2.sam

对输出数据的解读，字段解释

No. 名称 描述
1 QNAME Query NAME of the read or the read pair
2 FLAG Bitwise FLAG (pairing, strand, mate strand, etc.)
3 RNAME Reference sequence NAME
4 POS 1-Based leftmost POSition of clipped alignment
5 MAPQ MAPping Quality (Phred-scaled)
6 CIGAR Extended CIGAR string (operations: MIDNSHP)
7 MRNM Mate Reference NaMe (‘=’ if same as RNAME)
8 MPOS 1-Based leftmost Mate POSition
9 ISIZE Inferred Insert SIZE
10 SEQ Query SEQuence on the same strand as the reference
11 QUAL Query QUALity (ASCII-33=Phred base quality)