add more info on modes and standalone tools

README.md

@@ -1,11 +1,11 @@
 # About SPAdes
 
 SPAdes is a versatile toolkit designed for assembly and analysis of sequencing data.
-SPAdes is primarily developed for second-generation technologies (Illumina and IonTorrent), but most of its pipelines support hybrid mode, i.e. allow using long reads (PacBio and Oxford Nanopore) as a supplementary data.
+SPAdes is primarily developed for Illumina sequencing data, but can be used for IonTorrent as well. Most of SPAdes pipelines support hybrid mode, i.e. allow using long reads (PacBio and Oxford Nanopore) as a supplementary data.
 
 SPAdes package contains assembly pipelines for isolated and single-cell bacterial, as well as metagenomic and transcriptomic data.
 Additional modes allow to discover bacterial plasmids and RNA viruses, as well as perform HMM-guided assembly.
-Besides, SPAdes package includes supplementary tools for efficient k-mer counting and filtering, assembly graph construction and simplification, sequence-to-graph alignment and metagenomic binning refinement.
+Besides, SPAdes package includes supplementary tools for efficient k-mer counting and k-mer-based read filtering, assembly graph construction and simplification, sequence-to-graph alignment and metagenomic binning refinement.
 
 - [Complete SPAdes user manual](https://ablab.github.io/spades/)
 
@@ -46,7 +46,9 @@ Besides, SPAdes package includes supplementary tools for efficient k-mer countin
     bin/spades.py -1 left.fastq.gz -2 right.fastq.gz --pacbio pb.fastq -o output_folder
 ```
 
-- Available assembly modes: `--isolate`, `--sc`, `--plasmid`, `--meta`, `--metaplasmid`, `--metaviral`, `--rna`, `--rnaviral`, `--corona`, `--bio`.
+- Available assembly modes: `--isolate`, `--sc`, `--plasmid`, `--meta`, `--metaplasmid`, `--metaviral`, `--rna`, `--rnaviral`,  `--bio`, `--corona`, `--sewage`.
+
+- Standalone tools in SPAdes package: k-mer counting, k-mer cardinality estimation, k-mer-based read filtering, assembly graph construction, assembly graph simplification, alignment of long reads to an assembly graph, refinement of metagenomic binning.
 
 
 # Citation

docs/getting-started.md

@@ -12,6 +12,7 @@ SPAdes is an assembler for second-generation sequencing data (Illumina or IonTor
 ```
 
 ## Useful one-liners
+
 - A single paired-end library (separate files, gzipped):
 ``` bash
 bin/spades.py -1 left.fastq.gz -2 right.fastq.gz -o output_folder
@@ -56,8 +57,45 @@ bin/spades.py --rna -1 left.fastq.gz -2 right.fastq.gz -o output_folder
 bin/spades.py --rnaviral -1 left.fastq.gz -2 right.fastq.gz -o output_folder
 ```
 
-- Available assembly modes: `--isolate`, `--sc`, `--plasmid`, `--meta`, `--metaplasmid`, `--metaviral`, `--rna`, `--rnaviral`, `--corona`, `--bio`.
+## Available assembly modes
+
+- `--isolate` - converntional bacterial data;
+
+- `--sc` - single-cell bacterial data;
+
+- `--meta` - metagenome assembly;
+
+- `--plasmid` / `--metaplasmid` - plasmid discovery in conventional bacterial / metagenomic data;
+
+- `--metaviral` - viral assembly from metagenomic data;
+
+- `--rna` - transcriptome assembly (RNA-Seq);
+
+- `--rnaviral` - assembling viral RNA-Seq data;
+
+- `--bio` - assembly of non-ribosomal and polyketide gene clusters;
+
+- `--corona` - coronaviridae genome assembly;
+
+- `--sewage` - wastewater samples analysis.
+
+
+## Standalone SPAdes tools
+
+- `spades-kmercount` - k-mer counting;
+
+- `spades-read-filter` - read filtering using k-mer coverage;
+
+- `spades-kmer-estimating` - estimating number of unique k-mers;
+
+- `spades-gbuilder` - assembly graph construction;
+
+- `spades-gsimplifier` - assembly graph simplification;
+
+- `spalgner` - alignment of long reads to assembly graph;
 
+- `spades-gmapper` - specific alignment of long reads to assembly graph used in hybrid assembly pipeline;
 
+- `binspreader` - refinement of metagenome-assembled genomes.
 
 

docs/index.md

@@ -3,11 +3,11 @@
 ![SPAdes](spades.png){ align=right }
 
 SPAdes - St. Petersburg genome assembler - is a versatile toolkit designed for assembly and analysis of sequencing data.
-SPAdes is primarily developed for second-generation technologies (Illumina and IonTorrent), but most of its pipelines support hybrid mode, i.e. allow using long reads (PacBio and Oxford Nanopore) as a supplementary data.
+SPAdes is primarily developed for Illumina sequencing data, but can be used for IonTorrent as well. Most of SPAdes pipelines support hybrid mode, i.e. allow using long reads (PacBio and Oxford Nanopore) as a supplementary data.
 
 SPAdes package contains assembly pipelines for isolated and single-cell bacterial, as well as metagenomic and transcriptomic data.
 Additional modes allow to discover bacterial plasmids and RNA viruses, as well as perform HMM-guided assembly.
-Besides, SPAdes package includes supplementary tools for efficient k-mer counting and filtering, assembly graph construction and simplification, sequence-to-graph alignment and metagenomic binning refinement.
+Besides, SPAdes package includes supplementary tools for efficient k-mer counting and k-mer-based read filtering, assembly graph construction and simplification, sequence-to-graph alignment and metagenomic binning refinement.
 
 SPAdes version 3.15.5 was released under GPLv2 on July 14th, 2022 and can be downloaded [here](https://github.com/ablab/spades/releases/latest/).
 

docs/standalone.md

@@ -188,13 +188,13 @@ Additional options are:
 `-tmpdir <dir_name>  `
     scratch directory to use
 
-While `spades-mapper` is a solution for those who work on hybridSPAdes assembly and want to get exactly its intermediate results, [SPAligner](standalone.md#spaligner) is an end-product application for sequence-to-graph alignment with tunable parameters and output types.
+While `spades-gmapper` is a solution for those who work on hybridSPAdes assembly and want to get exactly its intermediate results, [SPAligner](standalone.md#spaligner) is an end-product application for sequence-to-graph alignment with tunable parameters and output types.
 
 
 ### SPAligner
 A tool for fast and accurate alignment of nucleotide sequences to assembly graphs. It takes file with sequences (in fasta/fastq format) and assembly in GFA format and outputs long read to graph alignment in various formats (such as tsv, fasta and [GPA](https://github.com/ocxtal/gpa "GPA-format spec")).
 
-Synopsis: `spaligner assembly/src/projects/spaligner_config.yaml -d <value> -s <value> -g <value> -k <value> [-t <value>] [-o <value>]`
+Synopsis: `spaligner src/projects/spaligner_config.yaml -d <value> -s <value> -g <value> -k <value> [-t <value>] [-o <value>]`
 
 Parameters are: