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DOC: Update README.md
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Vini2 committed Aug 23, 2023
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[![DOI](https://img.shields.io/badge/DOI-10.4230/LIPIcs.WABI.2020.8-informational)](https://doi.org/10.4230/LIPIcs.WABI.2020.8)
[![DOI](https://img.shields.io/badge/DOI-10.1186/s13015--021--00185--6-yellow)](https://doi.org/10.1186/s13015-021-00185-6)
[![DOI](https://zenodo.org/badge/262936904.svg)](https://zenodo.org/badge/latestdoi/262936904)

[![CI](https://github.com/metagentools/GraphBin2/actions/workflows/testing.yml/badge.svg)](https://github.com/metagentools/GraphBin2/actions/workflows/testing.yml)
![GitHub](https://img.shields.io/github/license/Vini2/GraphBin2)
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You can see the usage options of GraphBin2 by typing `./graphbin2 -h` on the command line. For example,

```
usage: graphbin2 [-h] --assembler ASSEMBLER --graph GRAPH --contigs CONTIGS
[--paths PATHS] [--abundance ABUNDANCE] --binned BINNED
--output OUTPUT [--prefix PREFIX] [--depth DEPTH]
[--threshold THRESHOLD] [--delimiter DELIMITER]
[--nthreads NTHREADS]
GraphBin2 Help. GraphBin2 is a tool which refines the binning results obtained
from existing tools and, more importantly, is able to assign contigs to
multiple bins. GraphBin2 uses the connectivity and coverage information from
assembly graphs to adjust existing binning results on contigs and to infer
contigs shared by multiple species.
optional arguments:
-h, --help show this help message and exit
--assembler ASSEMBLER
name of the assembler used (SPAdes, SGA or Flye)
--graph GRAPH path to the assembly graph file
--contigs CONTIGS path to the contigs file
--paths PATHS path to the contigs.paths file
--abundance ABUNDANCE
path to the abundance file
--binned BINNED path to the .csv file with the initial binning output
from an existing tool
--output OUTPUT path to the output folder
--prefix PREFIX prefix for the output file
--depth DEPTH maximum depth for the breadth-first-search. [default:
5]
--threshold THRESHOLD
threshold for determining inconsistent vertices.
[default: 1.5]
--delimiter DELIMITER
delimiter for input/output results. Supports a comma
(,), a semicolon (;), a tab ($'\t'), a space (" ") and
a pipe (|) [default: , (comma)]
--nthreads NTHREADS number of threads to use. [default: 8]
Usage: graphbin2 [OPTIONS]
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using
Assembly Graphs GraphBin2 is a tool which refines the binning results
obtained from existing tools and, is able to assign contigs to multiple
bins. GraphBin2 uses the connectivity and coverage information from
assembly graphs to adjust existing binning results on contigs and to infer
contigs shared by multiple species.
Options:
--assembler [spades|sga|flye] name of the assembler used. (Supports SPAdes,
SGA and Flye) [required]
--graph PATH path to the assembly graph file [required]
--contigs PATH path to the contigs file [required]
--paths PATH path to the contigs.paths (metaSPAdes) or
assembly.info (metaFlye) file
--abundance PATH path to the abundance file [required]
--binned PATH path to the .csv file with the initial
binning output from an existing toole
[required]
--output PATH path to the output folder [required]
--prefix TEXT prefix for the output file
--depth INTEGER maximum depth for the breadth-first-search.
[default: 5]
--threshold FLOAT threshold for determining inconsistent
vertices. [default: 1.5]
--delimiter [,|;|$'\t'|" "] delimiter for output results. Supports a
comma (,), a semicolon (;), a tab ($'\t'), a
space (" ") and a pipe (|) . [default: ,]
--nthreads INTEGER number of threads to use. [default: 8]
-v, --version Show the version and exit.
--help Show this message and exit.
```

## Input Format
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### Initial Binning Result
<p align="center">
<img src="https://raw.githubusercontent.com/metagentools/GraphBin/master/images/initial_binning_result.svg" width="500" title="Initial assembly graph" alt="Initial binning result">
<img src="https://raw.githubusercontent.com/metagentools/GraphBin2/master/images/initial_binning_result.svg" width="500" title="Initial assembly graph" alt="Initial binning result">
</p>

### Assembly Graph with Refined Labels
<p align="center">
<img src="https://raw.githubusercontent.com/metagentools/GraphBin/master/images/label_refined.svg" width="500" title="Initial assembly graph" alt="Labels refined">
<img src="https://raw.githubusercontent.com/metagentools/GraphBin2/master/images/label_refined.svg" width="500" title="Initial assembly graph" alt="Labels refined">
</p>

### Assembly Graph after Label Propagation
<p align="center">
<img src="https://raw.githubusercontent.com/metagentools/GraphBin/master/images/label_propagated.svg" width="500" title="Initial assembly graph" alt="Labels propagated">
<img src="https://raw.githubusercontent.com/metagentools/GraphBin2/master/images/label_propagated.svg" width="500" title="Initial assembly graph" alt="Labels propagated">
</p>

### Assembly Graph with Multi-labelled Vertices
<p align="center">
<img src="https://raw.githubusercontent.com/metagentools/GraphBin/master/images/multiple_marked.svg" width="500" title="Initial assembly graph" alt="Multi-labelled">
<img src="https://raw.githubusercontent.com/metagentools/GraphBin2/master/images/multiple_marked.svg" width="500" title="Initial assembly graph" alt="Multi-labelled">
</p>

## References
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