update version and docs, changelog draft

README.md

@@ -13,6 +13,7 @@ Besides, SPAdes package includes supplementary tools for efficient k-mer countin
 
 - [Latest SPAdes publication](https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.102)
 
+Current version: see `VERSION` file.
 
 # Quick start
 

VERSION

@@ -1 +1 @@
-3.16.0-dev
+4.0.0

changelog.md

@@ -1,5 +1,27 @@
 # SPAdes Genome Assembler changelog
 
+## SPAdes 4.0.0, 3 June 2024
+- Python3.8 is now a minimal required version, python2 is deprecated;
+- SPAdes now supports SRA files as input;
+- PathRacer is now released as a part of SPAdes package;
+- [BinSPreader](https://ablab.github.io/spades/binspreader.html) is also along with SPAdes package;
+- New gfa-split tool;
+- New [wasterwaterSPAdes](https://ablab.github.io/spades/running.html#-sewage) mode;
+- Native support for running on Apple Silicon processors;
+- Native support for running  on aarch64/linux;
+- Binaries are now built using ManyLinux 2.28;
+- Parallel & improved GapCloser algorithm;
+- Faster graph simplification;
+- Allow external projects integration with SPAdes;
+- Use SPOA for long reads consensus;
+- SPAdes outputs assembly graph in GFA v1.2 format by default, older v1.1 format is also available;
+- SPAdes tags circular paths in assembly graph with `TP:Z:circular` flag;
+- SPAdes now uses `zlib-ng` for faster gzip decompression of input files;
+- Fixed compilation with gcc 13;
+- Removed deprecated truSPAdes functionality;
+- Reworked and improved documentation;
+- Lots of other fixes and improvements.
+
 
 ## SPAdes 3.15.5, 14 July 2022
 

docs/getting-started.md

@@ -1,12 +1,13 @@
 # Quick start
 
+SPAdes assembler supports:
 
-- SPAdes assembler supports:
-  - Assembly of second-generation sequencing data (Illumina or IonTorrent);
-  - PacBio and Nanopore reads that are used as supplementary data only.
+- Assembly of second-generation sequencing data (Illumina or IonTorrent);
+- PacBio and Nanopore reads that are used as supplementary data only.
 
-- SPAdes allows to assemble genomes, metagenomes, transcriptomes, viral genomes etc.
+SPAdes allows to assemble genomes, metagenomes, transcriptomes, viral genomes etc.
 
+Current SPAdes version: {{ spades_version() }}.
 
 1. Download SPAdes binaries for
    [Linux](https://github.com/ablab/spades/releases/latest/) or [MacOS](https://github.com/ablab/spades/releases/latest/). 

docs/index.md

@@ -12,6 +12,6 @@ perform HMM-guided assembly and more. SPAdes package also includes supplementary
 k-mer counting and k-mer-based read filtering, assembly graph construction and simplification,
 sequence-to-graph alignment and metagenomic binning refinement.
 
-SPAdes version {{ spades_version() }} was released under GPLv2 on July 14th, 2022 and can be downloaded [here](https://github.com/ablab/spades/releases/latest/).
+SPAdes version {{ spades_version() }} was released under GPLv2 on June 3rd, 2024 and can be downloaded [here](https://github.com/ablab/spades/releases/latest/).
 
 The latest SPAdes paper describing various pipelines in a protocol format is available [here](https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.102).