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Add gsimplifier docs
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Itolstoganov authored and asl committed Apr 2, 2024
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`-spades `
output graph in SPAdes internal format

## Graph simplification

Graph simplification tool `spades-gsimplifier` has four mandatory options: the first one is an input graph in GFA format, or a prefix of the SPAdes internal graph pack format created by setting [checkpoint options](running.md#pipeline-options). The second one is the prefix of the output simplified graph. The last two are the k-mer size and the read length.

Synopsis: `spades-gsimplifier <graph. In GFA (ending with .gfa) or prefix to SPAdes graph pack> <output prefix> [--gfa] [--spades-gp] [--use-cov-ratios] -k <value> --read-length <value> [OPTION...]`

Additional options are:

`--gfa`
produce GFA output (default: true)

`--spades-gp`
produce output graph pack in the SPAdes internal format (default: false)

`--use-cov-ratios`
enable simplification procedures based on unitig coverage ratios (default: false)

`-k <value>`
k-mer length to use

`--read-length <value>`
read length to use

`-c, --coverage <coverage>`
estimated average (k+1-mer) bin coverage (default: 0.) or 'auto' (works only with '-d/--dead-ends' provided)

`-t, --threads <value>`
number of threads to use (default: max_threads / 2)

`-p, --profile <file>`
file with edge coverage profiles across multiple samples

`-s, --stop-codons <file>`
file with stop codon positions

`-d, --dead-ends <file>`
while processing a subgraph -- file listing edges which are dead-ends in the
original graph

## Long read to graph alignment

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Note that in order you use SPAligner one need either to use pre-built binaries or compiler SPAdes from sources using additional `-DSPADES_ENABLE_PROJECTS=spaligner` option.

# Binning refining using assembly graphs
## Binning refining using assembly graphs

BinSPreader is a tool that attempts to refine metagenome-assembled genomes (MAGs) obtained from existing tools. BinSPreader exploits the assembly graph topology and other connectivity information, such as paired-end and Hi-C reads, to refine the existing binning, correct binning errors, propagate binning from longer contigs to shorter contigs, and infer contigs belonging to multiple bins.

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