@@ -98,15 +98,14 @@ python SolidBin.py --contig_file /path/to/contigs.fasta --composition_profiles /
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```
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## Using GraphBin2
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- You can see the usage options of GraphBin2 by typing ``` python graphbin2.py -h`` ` on the command line. For example,
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+ You can see the usage options of GraphBin2 by typing ` ./graphbin2 -h` on the command line. For example,
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```
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- python graphbin2.py -h
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- usage: graphbin2.py [-h] --assembler ASSEMBLER --graph GRAPH --contigs CONTIGS
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- [--paths PATHS] [--abundance ABUNDANCE] --binned BINNED
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- --output OUTPUT [--prefix PREFIX] [--depth DEPTH]
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- [--threshold THRESHOLD] [--delimiter DELIMITER]
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- [--nthreads NTHREADS]
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+ usage: graphbin2 [-h] --assembler ASSEMBLER --graph GRAPH --contigs CONTIGS
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+ [--paths PATHS] [--abundance ABUNDANCE] --binned BINNED
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+ --output OUTPUT [--prefix PREFIX] [--depth DEPTH]
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+ [--threshold THRESHOLD] [--delimiter DELIMITER]
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+ [--nthreads NTHREADS]
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GraphBin2 Help. GraphBin2 is a tool which refines the binning results obtained
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from existing tools and, more importantly, is able to assign contigs to
@@ -134,8 +133,8 @@ optional arguments:
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[default: 1.5]
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--delimiter DELIMITER
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delimiter for input/output results. Supports a comma
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- (,), a semicolon (;), a tab ($'\t'), a space ( ) and a
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- pipe (|) [default: , (comma)]
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+ (,), a semicolon (;), a tab ($'\t'), a space (" " ) and
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+ a pipe (|) [default: , (comma)]
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--nthreads NTHREADS number of threads to use. [default: 8]
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```
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