GraphBin-Tk combines assembly graph-based metagenomic bin-refinement and binning techniques GraphBin, GraphBin2 and MetaCoAG into one comprehensive toolkit.
Run gbintk --help or gbintk -h to list the help message for GraphBin-Tk.
Usage: gbintk [OPTIONS] COMMAND [ARGS]...
gbintk (GraphBin-Tk): Assembly graph-based metagenomic binning toolkit
Options:
-v, --version Show the version and exit.
-h, --help Show this message and exit.
Commands:
graphbin GraphBin: Refined Binning of Metagenomic Contigs using...
graphbin2 GraphBin2: Refined and Overlapped Binning of Metagenomic...
metacoag MetaCoAG: Binning Metagenomic Contigs via Composition,...gbintk graphbin: Run GraphBin
Run gbintk graphbin --help or gbintk graphbin -h to list the help message for GraphBin.
Usage: gbintk graphbin [OPTIONS]
GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs
Options:
--assembler [spades|sga|megahit|flye]
name of the assembler used (SPAdes, SGA,
MEGAHIT or 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
--binned PATH path to the .csv file with the initial
binning output from an existing tool
[required]
--output PATH path to the output folder [required]
--prefix TEXT prefix for the output file
--max_iteration INTEGER maximum number of iterations for label
propagation algorithm [default: 100]
--diff_threshold FLOAT RANGE difference threshold for label propagation
algorithm [default: 0.1; 0<=x<=1]
--delimiter [,|;|$'\t'|" "] delimiter for input/output results. Supports
a comma (,), a semicolon (;), a tab ($'\t'),
a space (" ") and a pipe (|) [default: ,]
-h, --help Show this message and exit.gbintk graphbin2: Run GraphBin2
Run gbintk graphbin2 --help or gbintk graphbin2 -h to list the help message for GraphBin2.
Usage: gbintk graphbin2 [OPTIONS]
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using
Assembly Graphs
Options:
--assembler [spades|sga|megahit|flye]
name of the assembler used (SPAdes, SGA,
MEGAHIT or 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 tool
[required]
--output PATH path to the output folder [required]
--prefix TEXT prefix for the output file
--depthb INTEGER maximum depth for the breadth-first-search.
[default: 5]
--threshold FLOAT threshold for determining inconsistent
vertices. [default: 1.5]
--delimiter [,|;|$'\t'|" "] delimiter for input/output results. Supports
a comma (,), a semicolon (;), a tab ($'\t'),
a space (" ") and a pipe (|) [default: ,]
--nthreads INTEGER number of threads to use. [default: 8]
-h, --help Show this message and exit.gbintk metacoag: Run MetaCoAG
Run gbintk metacoag --help or gbintk metacoag -h to list the help message for MetaCoAG.
Usage: gbintk metacoag [OPTIONS]
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly
Graphs
Options:
--assembler [spades|sga|megahit|flye]
name of the assembler used (SPAdes, SGA,
MEGAHIT or 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]
--output PATH path to the output folder [required]
--hmm TEXT path to marker.hmm file. [default:
auxiliary/marker.hmm]
--prefix TEXT prefix for the output file
--min_length INTEGER minimum length of contigs to consider for
binning. [default: 1000]
--p_intra FLOAT RANGE minimum probability of an edge matching to
assign to the same bin. [default: 0.1;
0<=x<=1]
--p_inter FLOAT RANGE maximum probability of an edge matching to
create a new bin. [default: 0.01; 0<=x<=1]
--d_limit INTEGER distance limit for contig matching.
[default: 20]
--depthlp INTEGER depth to consider for label propagation.
[default: 10]
--n_mg INTEGER total number of marker genes. [default:
108]
--no_cut_tc do not use --cut_tc for hmmsearch.
--mg_threshold FLOAT RANGE length threshold to consider marker genes.
[default: 0.5; 0<=x<=1]
--bin_mg_threshold FLOAT RANGE minimum fraction of marker genes that should
be present in a bin. [default: 0.33333;
0<=x<=1]
--min_bin_size INTEGER minimum size of a bin to output in base
pairs (bp). [default: 200000]
--delimiter [,|;|$'\t'|" "] delimiter for input/output results. Supports
a comma (,), a semicolon (;), a tab ($'\t'),
a space (" ") and a pipe (|) [default: ,]
--nthreads INTEGER number of threads to use. [default: 8]
-h, --help Show this message and exit.GraphBin-Tk is funded by an Essential Open Source Software for Science Grant from the Chan Zuckerberg Initiative.
