macでインフォマティクス

macでインフォマティクス

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

 

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

 

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

 

関連