hifiasm软件使用 (1)市场上绝大多数二倍体基因组,只需要组装2n中的n,所以参数一般给 -l 2 -n 4: hifiasm -o test.asm -t 16 -l 2 -n 4 HiFi-reads.fa.gz 2> test.assemble.log #-t16为16线程,test.ccs.fa.gz为处理好的ccs数据,可为fasta或者fastq,用法很简单 (2)对于二倍体,结合HiC数据拆单...
Hifiasm输出的gfa格式的组装图文件,大致遵循GFA 1.0格式规范,但有几个Hifiasm特有的内容。 gfa文件第一列表示序列图的类型(通常有S,L,A几种类型)。 S表示Segment,L表示Link。Hifiasm输出的gfa格式还有一种特有的A类型的行,用来保存用于构建contig/unitig的reads的信息。 S (Segment) 行: S 行示例:S ptg000001l...
1.2. Hifiasm的基础命令 1.3. Hifiasm的输出文件 1.3.1. 输出文件 对于输出的每个图（graph），Hifiasm也输出简化版本（xx_nnoseq_xx.gfa），此文件无易视序列。低质量区域坐标写入lowQ.bed文件。1.3.2. 输出文件格式 Hifiasm输出的gfa格式组装图，遵循GFA 1.0规范，特有内容包含S、L、A类型表...
-o:定义输出文件的文件名前缀, -t:线程数 get primary contigs in FASTA 提取数据 awk'/^S/{print ">"$2;print $3}'GX.HiFi.fq.gz>test.p_ctg.fa 下载fasta文件 test.p_ctg.fa 与基因组文件比对 homozygous genomes Assemble inbred/homozygous genomes (-l0 disables duplication purging) hifiasm -o ...
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Hifiasm purges haplotig duplications by default. For inbred or homozygous genomes, you may disable purging with option-l0. Old HiFi reads may contain short adapter sequences at the ends of reads. You can specify-z20to trim both ends of reads by 20bp. For small genomes, use-f0to disable...
Hifiasm purges haplotig duplications by default. For inbred or homozygous genomes, you may disable purging with option-l0. Old HiFi reads may contain short adapter sequences at the ends of reads. You can specify-z20to trim both ends of reads by 20bp. For small genomes, use-f0to disable...
gfa文件第一列表示序列图的类型(通常有S,L,A几种类型)。 S表示Segment,L表示Link。Hifiasm输出的gfa格式还有一种特有的A类型的行,用来保存用于构建contig/unitig的reads的信息。 S (Segment) 行: S 行示例:S ptg000001l ATTTGG... LN:i:17404864 rd:i:41 ...
(-l0 disables duplication purging) hifiasm -o CHM13.asm -t32 -l0 CHM13-HiFi.fa.gz 2> CHM13.asm.log # Assemble heterozygous genomes with built-in duplication purging hifiasm -o HG002.asm -t32 HG002-file1.fq.gz HG002-file2.fq.gz # Hi-C phasing with paired-end short reads in ...
Hifiasm purges haplotig duplications by default. For inbred or homozygous genomes, you may disable purging with option-l0. Old HiFi reads may contain short adapter sequences at the ends of reads. You can specify-z20to trim both ends of reads by 20bp. For small genomes, use-f0to disable...