首先,hifiasm-meta具有读长选择步骤,可以减少高丰度菌株的覆盖率,而不会丢失低丰度菌株的数据。其次,在组装图的构建过程中,hifiasm-meta试图保护低覆盖率基因组中的序列,这些序列可能被视为嵌合序列并被原始hifiasm丢弃。第三,hifiasm-meta 只有在推断出与读长完全重叠的其他序列来自同一单倍型时,才会丢弃包含的序列,这...
hifiasm-meta是基于hifiasm的宏基因组组装工具：改善了一些宏基因组数据中比单样本测序更突出的问题（例如contained reads）；优先于获得连贯的contigs，过程不需要手工干预，和hifiasm相同是一个binary和一行命令；对于回收variants和SV，可能对read-contig的alignment+variant calling比处理assemblygraph更实用）；（可选）...
这表明hifiasm-meta更擅长解决细微的组分差异。 图3人肠道样本宏基因组hifiasm-meta组装结果 最后,作者比较了软件的性能,hifiasm-meta组装sheepA和鸡数据集需要48个CPU大约18个小时,而人类肠道样本花费了大约3个小时,与metaFlye速度相当,并且始终比HiCanu软件快好几倍。 综上,hifiasm-meta软件将进一步推动宏基因组组装。
A hifiasm fork for metagenome assembly using Hifi reads. Getting Started #Install hifiasm-meta (g++ and zlib required)git clone https://github.com/xfengnefx/hifiasm-meta.gitcdhifiasm-meta&&make#Runhifiasm_meta -t32 -o asm reads.fq.gz2>asm.log hifiasm_meta -t32 --force-rs -o asm read...
# Install hifiasm-meta (g++ and zlib required) git clone https://github.com/xfengnefx/hifiasm-meta.git cd hifiasm-meta && make # Run hifiasm_meta -t32 -oasm reads.fq.gz 2>asm.log hifiasm_meta -t32 -S -o asm reads.fq.gz 2>asm.log // if the dataset has high redundancy, or...
De novo assembly of metagenome samples is a common approach to the study of microbial communities. Current metagenome assemblers developed for short sequence reads or noisy long reads were not optimized for accurate long reads. We thus developed hifiasm-meta, a metagenome assembler that exploits the...
哈佛大学医学院Dana-Farber癌症研究所李恒课题组重磅推出三代HiFi宏基因组组装软件——hifiasm-meta。研究论文“Metagenome assembly of high-fidelity long reads with hifiasm-meta”预印本在线发布。 宏基因组样本的do novo组装是研究微生物群落的常用方法。与单个物种的组装相比,宏基因组组装存在PacBio HiFi 数据中...
hifiasm-meta的工作流程包括可自定义的读长输入、序列纠错、序列重叠信息查找、字符串图构建和组装图清理。纠错和序列重叠步骤与原始 hifiasm 基本相同。我们添加了可选的读长选择,并改进了其余步骤。 ② 输入读长的可选下采样 如果启用了读长选择,hifiasm-meta首先粗略地猜测对于整个数据集是否有太多的对齐计算要执行...
hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. - hifiasm-meta/Assembly.h at meta · xfengnefx/hifiasm-meta
(WIP) A hifiasm fork (https://github.com/chhylp123/hifiasm) for metagenome assembly. Getting Started # Install hifiasm-meta (g++ and zlib required) git clone https://github.com/xfengnefx/hifiasm-meta.git cd hifiasm-meta && make # Run hifiasm_meta -t32 -oasm reads.fq.gz 2>asm.log...