qazwsx1995 / hifiasm-meta Goto Github PK

(WIP) A hifiasm fork (https://github.com/chhylp123/hifiasm) for metagenome assembly.

# 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 overlap & error correction takes way too long

Raw unitig graph: asm.r_utg*.gfa

Cleaned unitig graph: asm.p_utg*.gfa

Contig graph: asm.p_ctg*.gfa and asm.a_ctg*.gfa

Unitig/Contig naming: ^s[0-9]+\.[uc]tg[0-9]{6}[lc] where the s[0-9]+ is a subgraph label.

Based on the limited available test data, real datasets are unlikely to require read selection; mock datasets, however, might need it.

Non-release commits may have extra debug outputs for dev/debug purposes, even without -V.

Bin file is one-way compatible with the stable hifiasm for now: stable hifiasm can use hifiasm_meta's bin file, but not vice versa. Meta needs to store extra info from overlap & error correction step.

See also README_ha.md, the stable hifiasm doc.

#Interface
-B		Name of bin files. Allows to use bin files from other 
       		directories.

# Read selection
-S		Enable read selection.
--force-preovec Force kmer frequency-based read selection. 
                (otherwise if total number of read overlaps 
                 look realistic, won't do selection.)
--lowq-10Lower  10% quantile kmer frequency threshold, runtime. Lower value means less reads kept, if read selection is triggered. [150]

Read selection needs to speed up. Currently there's a blocking sequential step.

Sheep fecal material dataset: wall clock 17.2 h on 48 cpus, peak memory 183.3 GB.

A Bandage plot of primary contig graph:

Mock community ATCC MSA-1003 (with -S --lowq-10 50)

*: not one clean circle.

Mock community Zymo D6331, standard input library: wall clock 15.7 h on 32 cpus, peak memory 121.7 GB.

*: E.coli strains except B2207 and B766 presented in one subgraph.