From ea3edbaf049f74161942fe3bd65101454ed2331d Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Wed, 23 Aug 2023 11:32:58 +0930 Subject: [PATCH] DOC: Update README.md --- README.md | 76 +++++++++++++++++++++++++++---------------------------- 1 file changed, 37 insertions(+), 39 deletions(-) diff --git a/README.md b/README.md index 188c942..0fe067d 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,7 @@ [![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) @@ -121,41 +122,38 @@ python SolidBin.py --contig_file /path/to/contigs.fasta --composition_profiles / 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 @@ -236,22 +234,22 @@ graphbin2 --assembler flye --contigs /path/to/edges.fasta --abundance /path/to/a ### Initial Binning Result

- Initial binning result + Initial binning result

### Assembly Graph with Refined Labels

- Labels refined + Labels refined

### Assembly Graph after Label Propagation

- Labels propagated + Labels propagated

### Assembly Graph with Multi-labelled Vertices

- Multi-labelled + Multi-labelled

## References