2021 10/19 プレプリント引用
2023/07/06 追記
現在のメタゲノムアセンブラは、ショートシーケンスリードやノイズの多いロングリード用に開発されたもので、正確なロングリードには最適化されていない。ここでは、最近のデータの高い精度を利用した新しいメタゲノムアセンブラであるhifiasm-metaを紹介する。7つの経験的データセットで評価した結果，hifiasm-metaは，1つのデータセットにつき数十から数百の完全な環状の細菌ゲノムを再構築し，他のメタゲノムアセンブラよりも一貫して優れていた。
Hifiasm-metaはメタゲノムアセンブリのためのhifiasmの forkである。
Our lab @lh3lh3 developed a metagenome assembler, hifiasm-meta (https://t.co/iEFeLhK3xn), which reconstructs @PacBio Hifi libraries to tens to hundreds of complete circular bacterial genomes. We hope these high-quality contigs to offer a new means to study microbial communities.
— Xiaowen Feng (@0xfxfxf) October 19, 2021
Preprint on hifiasm-meta, a metagenome assembler for @PacBio HiFi reads. 245 >1Mb circular contigs from a single ultra-deep sample. 75 from omnivore-vegan gut co-assembly. Sharp omnivore/vegan separation at the contig level but not at the genus level. Led by @0xfxfxf. https://t.co/KMRE5Fm3kT pic.twitter.com/CIHZsPgSHx
— Heng Li (@lh3lh3) October 19, 2021
インストール
git clone https://github.com/xfengnefx/hifiasm-meta.git
cd hifiasm-meta && make
> ./hifiasm_meta
$ ./hifiasm_meta
Usage: hifiasm_meta 0.1-r037 (hifiasm code base 0.13-r308)
Options:
Input/Output:
-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.
--force-preovec
enable and force read selection.
--lowq-10
lower 10% runtime kmer frequency threshold. [50]
--lowq-5
lower 5% runtime kmer frequency threshold. [50]
--lowq-3
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]
Assembly:
-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]
Auxiliary:
-e ban assembly, i.e. terminate before generating string graph
--write-paf dump overlaps (paf).
--dump-all-ovlp
dump all overlaps ever calculated in the final overlapping (paf).
--write-ec
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.
実行方法
HiFi readを指定する
hifiasm_meta -o asm -t 32 asm.fq.gz 2>log
引用
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
関連
2023/07/06
New benchmarks are out, comparing @PacBio HiFi #metagenome assembly methods.
— Daniel Portik (@DPortik) July 5, 2023
Each method has unique strengths, but main conclusion is:
"hifiasm-meta produced the most contiguous and complete assembly among all the tools, followed by metaFlye and HiCanu"https://t.co/XS9ODAdY5D
" (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。"
