From c7453c45b97fefc22e4e6dbc5341c13d1bf46edf Mon Sep 17 00:00:00 2001 From: Itolstoganov Date: Mon, 11 Mar 2024 16:43:11 +0100 Subject: [PATCH] Add gsimplifier docs --- docs/standalone.md | 39 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) diff --git a/docs/standalone.md b/docs/standalone.md index e02a46c22..47dd4a0d2 100644 --- a/docs/standalone.md +++ b/docs/standalone.md @@ -133,7 +133,44 @@ Additional options are: `-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 [--gfa] [--spades-gp] [--use-cov-ratios] -k --read-length [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 ` + k-mer length to use + +`--read-length ` + read length to use + +`-c, --coverage ` + estimated average (k+1-mer) bin coverage (default: 0.) or 'auto' (works only with '-d/--dead-ends' provided) + +`-t, --threads ` + number of threads to use (default: max_threads / 2) + +`-p, --profile ` + file with edge coverage profiles across multiple samples + +`-s, --stop-codons ` + file with stop codon positions + +`-d, --dead-ends ` + while processing a subgraph -- file listing edges which are dead-ends in the + original graph ## Long read to graph alignment @@ -189,7 +226,7 @@ Also if you want to align protein sequences please refer to our [pre-release ver 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.