HTS (NGS) 関連のインフォマティクス情報についてまとめています。

メタゲノムのアセンブリを行う hifiasm-meta

2021 10/19 プレプリント引用

2023/07/06 追記




Hifiasm-metaはメタゲノムアセンブリのためのhifiasmの forkである。




git clone
cd hifiasm-meta && make

> ./hifiasm_meta 

$ ./hifiasm_meta 

Usage: hifiasm_meta 0.1-r037 (hifiasm code base 0.13-r308)



-o STR prefix of output files [hifiasm_meta.asm]

-B STR prefix of bin files, if it's different from -o [hifiasm_meta.asm]

-i ignore saved read correction and overlaps

-t INT number of threads [1]

-z INT length of adapters that should be removed [0]

--version show version number

Read selection:

-S enable read selection.


enable and force read selection.


lower 10% runtime kmer frequency threshold. [50]


lower 5% runtime kmer frequency threshold. [50]


lower 3% runtime kmer frequency threshold. [-1]

Overlap/Error correction:

-k INT k-mer length (must be <64) [51]

-w INT minimizer window size [51]

-f INT number of bits for bloom filter; 0 to disable [37]

-D FLOAT drop k-mers occurring >FLOAT*coverage times [5.0]

-N INT consider up to max(-D*coverage,-N) overlaps for each oriented read [100]

-r INT round of correction [3]


-a INT round of assembly cleaning [4]

-n INT remove tip unitigs composed of <=INT reads [3]

-x FLOAT max overlap drop ratio [0.8]

-y FLOAT min overlap drop ratio [0.2]


-e ban assembly, i.e. terminate before generating string graph

--write-paf dump overlaps (paf).


dump all overlaps ever calculated in the final overlapping (paf).


dump error corrected reads (fasta).

Example: ./hifiasm_meta -o asm -t 32 asm.fq.gz 2>log

See `man ./hifiasm_meta.1` for detailed descriptions command-line options.




HiFi readを指定する

hifiasm_meta -o asm -t 32 asm.fq.gz 2>log



GitHub - lh3/hifiasm-meta: Hifiasm: a haplotype-resolved assembler for accurate Hifi reads


2021 10/19

Metagenome assembly of high-fidelity long reads with hifiasm-meta
Xiaowen Feng, Haoyu Cheng, Daniel Portik, Heng Li

arXiv, Submitted on 16 Oct 2021




Comprehensive Assessment of Eleven de novo HiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes | bioRxiv

" (i)3つの真核生物ゲノムのリアルデータ、(ii)倍数性、シーケンスカバレッジレベル、ヘテロ接合率、シーケンスエラー率が異なる34の合成データセット、(iii)1つのリアルメタゲノムデータセット、(iv)組成存在量とヘテロ接合率が異なる5つの合成メタゲノムデータセットについて、11のde novo HiFiアセンブラの性能を評価した。"