介绍
megahit用于宏基因组测序数据的组装。组装速度较快,消耗资源较低。
输入
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,
min contig length : 组装的最小contig长度,长度小的contig将被舍去
k-min :最小kmer长度
k-max :最大kmer长度
k setp :kmer变化梯度值
结果
final.contigs.fa,
例如,
>k97_872 flag=0 multi=67.7803 len=320
GCCTGCGCCTCGATCGGATCACCCAGCCTCGTCCCCGTCCCATGCGCCTCCACCACATCCACCTCGGACGCCGACACCCCCGCGTTCTCCAACGCCCGCCGGATCACCCGCTGCTGCGACGGACCATTCGGCGCCATCAACCCATTCGACGCACCATCCTGATTCACCGCCGAACCACGCACCACCGCCAACACCCGATGCCCAAAACGACGAGCATCCGACAAACGCTCCACCACCAACACACCCACACCCTCACCCCAACCCGTCCCATCAGC
CCCCTCGGCAAACGACCTGCACCGACCATCAACCGACAACCCGCG