# 介绍

Hifiasm 是一款针对PacBio Hifi reads单倍体解析的快速从头组装工具

仓库地址

https://github.com/chhylp123/hifiasm

文章

https://arxiv.org/pdf/2008.01237.pdf

# 软件安装及测试

# 安装方法

# Install hifiasm (requiring g++ and zlib)
git clone https://github.com/chhylp123/hifiasm
cd hifiasm && make

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# 小测试数据下载

wget https://github.com/chhylp123/hifiasm/releases/download/v0.7/chr11-2M.fa.gz

大数据：小鼠数据

# 测试数据运行

针对小数据使用-f0

./hifiasm -o test -t4 -f0 chr11-2M.fa.gz 2> test.log

从gfa文件获得primary contigs

awk '/^S/{print ">"$2;print $3}' test.p_ctg.gfa > test.p_ctg.fa

# 软件参数

-l0 ：关掉 duplication purging，对于近交或者纯合基因组，建议加上该参数。
-t ：CPU 线程
-o ：输出文件的前缀
-z20 : 一些旧的HiFi reads可能会存在短的接头，使用该参数进行修剪
-f0 : 对于小基因组，该参数可以关闭起始bloom filter(该步骤会在开始时消耗16G内存)
-f38/-f39 : 如果基因组大于人类，建议使用该参数以节省内存

# Trio binning组装

Trio binning使用来自两个亲本基因组的reads，首先将来自后代的长读段划分为单倍型特异性集。然后将每个单体型独立组装，以完成完整的二倍体重建。

Trio binning assembly (requiring https://github.com/lh3/yak)

yak count -b37 -t16 -o pat.yak <(cat pat_1.fq.gz pat_2.fq.gz) <(cat pat_1.fq.gz pat_2.fq.gz)
yak count -b37 -t16 -o mat.yak <(cat mat_1.fq.gz mat_2.fq.gz) <(cat mat_1.fq.gz mat_2.fq.gz)
hifiasm -o HG002.asm -t32 -1 pat.yak -2 mat.yak HG002-HiFi.fa.gz

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# 输出结果

# non-trio assembly

Haplotype-resolved raw unitig graph in GFA format (prefix.r_utg.gfa). 保留了所有单倍体信息，包括一些体细胞突变和测序错误。
Haplotype-resolved processed unitig graph without small bubbles (prefix.p_utg.gfa). 相对于raw unitig，去除了图上的小气泡；这些小气泡可能是由于体细胞突变和数据里噪音引起的，不是真正的单倍体信息
Primary assembly contig graph (prefix.p_ctg.gfa). 折叠了不同的单倍型。
Alternate assembly contig graph (prefix.a_ctg.gfa). This graph consists of all assemblies that are discarded in primary contig graph.

# trio assembly

Haplotype-resolved raw unitig graph in GFA format (prefix.r_utg.gfa). This graph keeps all haplotype information.
Phased paternal/haplotype1 contig graph (prefix.hap1.p_ctg.gfa). This graph keeps the phased paternal/haplotype1 assembly.
Phased maternal/haplotype2 contig graph (prefix.hap2.p_ctg.gfa). This graph keeps the phased maternal/haplotype2 assembly.

Hifiasm writes error corrected reads to the prefix.ec.bin binary file and writes overlaps to prefix.ovlp.source.bin and prefix.ovlp.reverse.bin.

Purging haplotig duplications may introduce misassemblies.

# 组装软件比较

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# 其他

# HiFi 组装实例

The following table shows the statistics of several hifiasm primary assemblies:

_Dataset	_Size	_Cov.	_{Asm options}	_{CPU time}	_{Wall time}	_RAM	_N50
_{Mouse (C57/BL6J)}	_2.6Gb	_×25	_{-t48 -l0}	_172.9h	_4.8h	_76G	_21.1Mb
_{Maize (B73)}	_2.2Gb	_×22	_{-t48 -l0}	_203.2h	_5.1h	_68G	_36.7Mb
_Strawberry	_0.8Gb	_×36	_{-t48 -D10}	_152.7h	_3.7h	_91G	_17.8Mb
_Frog	_9.5Gb	_×29	_-t48	_2834.3h	_69.0h	_463G	_9.3Mb
_Redwood	_35.6Gb	_×28	_-t80	_3890.3h	_65.5h	_699G	_5.4Mb
_{Human (CHM13)}	_3.1Gb	_×32	_{-t48 -l0}	_310.7h	_8.2h	_114G	_88.9Mb
_{Human (HG00733)}	_3.1Gb	_×33	_-t48	_269.1h	_6.9h	_135G	_69.9Mb
_{Human (HG002)}	_3.1Gb	_×36	_-t48	_305.4h	_7.7h	_137G	_98.7Mb

Hifiasm can assemble a 3.1Gb human genome in several hours or a ~30Gb hexaploid redwood genome in a few days on a single machine. For trio binning assembly:

_Dataset	_Cov.	_{CPU time}	_{Elapsed time}	_RAM	_N50
_{HG00733, [father], [mother]}	_×33	_269.1h	_6.9h	_135G	_{35.1Mb (paternal), 34.9Mb (maternal)}
_{HG002, [father], [mother]}	_×36	_305.4h	_7.7h	_137G	_{41.0Mb (paternal), 40.8Mb (maternal)}
_{NA12878, [father], [mother]}	_×30	_180.8h	_4.9h	_123G	_{27.7Mb (paternal), 27.0Mb (maternal)}

Except NA12878, the assemblies above were produced by hifiasm v0.12 and can be downloaded at

ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/hifiasm-0.12/

NA12878 was assembled with an older version of hifiasm and is available at

ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/

# 帮助

For detailed description of options, please see man ./hifiasm.1. The -h option of hifiasm also provides brief description of options. If you have further questions, please raise an issue at the issue page.

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