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update readme.
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xfengnefx committed Dec 26, 2020
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Expand Up @@ -8,14 +8,14 @@ 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
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
```

## About this fork

Hifiasm_meta comes with a read selection module, which enables the assembly of dataset of high redundancy without compromising overall assembly quality, and meta-centric graph cleaning modules. It also handles chimeric read detection and contained reads etc more carefully in the metagenome assembly context, which, in some cases, could benefit the less represented species in the sample. We need more test samples to improve the heuristics.
Hifiasm\_meta comes with a read selection module, which enables the assembly of dataset of high redundancy without compromising overall assembly quality, and meta-centric graph cleaning modules. It also handles chimeric read detection and contained reads etc more carefully in the metagenome assembly context, which, in some cases, could benefit the less represented species in the sample. We need more test samples to improve the heuristics.

Currently hifiasm_meta does not take bining info.
Currently hifiasm\_meta does not take bining info.

## Output files

Expand Down Expand Up @@ -125,4 +125,4 @@ A [Bandage](https://github.com/rrwick/Bandage) plot of primary contig graph:
<sub>Escherichia coli B3008</sub>|<sub>8.25%</sub>|<sub>unseparated\*</sub>|<sub></sub>|<sub>Veillonella rogosae</sub>|<sub>11.02%</sub>|<sub>pass</sub>
<sub>Escherichia coli B766</sub>|<sub>7.83%</sub>|<sub>pass</sub>|<sub></sub>|<sub></sub>|<sub></sub>|<sub></sub>

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

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