介绍
bowtie2先对参考序列建索引,然后比对生成sam文件,samtools软件再将sam转为bam文件
输入
基因组序列文件:
fasta格式,例如
>seqname
AAAAAAAAGCTACTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTC
fq1文件:左端reads的fastq数据
格式例如,
@A00151:255:HNMLKDSXY:4:1101:8314:7467 1:N:0:TGAGGC
GTCACGCCGTCTCCTCATCTCGGCTCTCTCACCATGCAGTGGTCGAGGGCCGCGCTTTCTTACACCCGGGGAGAGGGGATTCCGGGCGGCGGGGTGCCCGGGACGAGGGAGGCCGGTGCCGCCGCGTTGCCGGCCGCGGGACGCGGTTGCC
+
FFFFFFFFFFFFF,:,FFFFFFFFFF:FFFFFFFF,FF:F,,FFFFFF,FFF::FF,:FF::F,FF,,FFFFF,,::FFFFFFFFFFFF::FFFFFFF:FF:FFFFF:FFFFFF::FF:FFFF:FFFFF:F:FFFFF,:,:F,FFFF,,:F
fq2文件:右端reads的fastq数据
格式例如,
@A00151:255:HNMLKDSXY:4:1101:8314:7467 2:N:0:TGAGGC
GGACGTCCCCATGGAGCTCCTGAGCTTACGCAGCGCCGCACGGCAACCGCGTCCGGCGTCGGCAACCGCGTCCGGTGCCCAACCGCGTCCAACGGCCGGCAACCGCGTCCCGCGGCCGGCACCGCGGCGGCACCGGCCTCCCTCGTCCCGG
+
F::F:F:FFFF:FFFFFFFF:FFFFF:FFFFFFFFFF,FFFFF:FFFFFFF,:FF,FFFFFFFF,FFFFF:FF:F::FF,FF:F,FFFFFFF,F::FF,FFFFFFFFFFF,FFF:FF:FFF,FFFFFFFFFFFFF::FF:FF:FF:FFFF,
结果
bam文件:比对结果文件,sam文件的二进制压缩文件