Flye 2.9.6 release (2 May 2025)
==============================
* Minor fix release, most assmeblies should not change
* Fixed rare race condition in polishing stage
* R10 ONT parameters (3% error) are now default for --nano-hq

Flye 2.9.5 release (27 Aug 2024)
===============================
* Python 3.12 support, Python 2 dropped

Flye 2.9.4 release (14 May 2024)
===============================
* Minor technical changes

Flye 2.9.3 release (28 November 2023)
====================================
* Disjointig step speedup for `--nano-hq` mode
* Improved `--keep-haplotypes` mode preserves more heterozygous SVs
* A few bug fixes

Flye 2.9.2 release (18 March 2023)
=================================
* Update to minimap 2.24 + using HiFi and Kit14 parameters for faster alignment
* Fixed a few small bugs and corner cases
* Polisher now outputs read depth for each base of consensus (can be used as confidence measure)

Flye 2.9.1 release (07 Aug 2022)
===============================
* New option --no-alt-contigs to remove all non-primary contigs from the assembly
* Fixed crash on MacOS with Python 3.8+
* Fixed rare artificially introduced mismatches while polishing
* Fixed slow simplification of very tangled graphs
* Various other small fixes

Flye 2.9 release (20 Aug 2022)
=============================
* Better assembly of very short sequences (e.g. plasmids or viruses). They vere often missed in previous versions.
* New --nano-hq mode for ONT Guppy5+ SUP and Q20 reads (3-5% error rate)
* Optimized default parameters for HiFi (HPC error threshold 0.01 -> 0.001; increased min overlap)
* Polishing improvements: reduced number of possible clusters of errors
* Improvements in repeat delection algorithm to further limit a chance of (otherwise infrequent) misassemblies
* Scaffolding is no longer performed by default (could be enabled with --scaffold)
* Bam file input for the standalone polisher (same interface as for FASTA/Q)
* Automatically selected minimum overlap up to 10k (was 5k)
* Discontinued --plasmid option due to the improvements in short sequences assembly
* --trestle and --subassemblies modes are now deprecated, and will be removed in the future versions
* New --extra-params option to modify config-level parameters
* Contig paths output in Gfa + number of reads supporting each link (RC tag)
* Update to minimap 2.18
* Several rare bug fixes/other improvements

Flye 2.8.3 release (10 Feb 2021)
===============================
* Reduced RAM consumption for some ultra-long ONT datasets
* Fixed rare artifical sequence insertions on some ONT datasets
* Asseemblies should be largely identical to 2.8

Flye 2.8.2 release (12 Dec 2020)
===============================
* Improvements in GFA output, much faster generation of large and tangled graphs
* Speed improvements for graph simplification algorithms
* A few minor bugs fixed
* Assemblies should be largely identical to 2.8

Flye 2.8.1 release (02 Sep 2020)
===============================
* Added a new option `--hifi-error` to control the expected error rate of HiFi reads (no other changes)

Flye 2.8 release (04 Aug 2020)
==============================
* Improvements in contiguity and speed for PacBio HiFi mode
* Using the `--meta` k-mer selection strategy in isolate assemblies as well.
This strategy is more robust to drops in coverage/contamination and reqires less memory
* 1.5-2x RAM footprint reduction for large assemblies (e.g. human ONT assembly now uses 400-500 Gb)
* Genome size parameter is no longer required (it is still needed for downsampling though `--asm-coverage`)
* Flye now can occasionally use overlaps shorter than "minOverlap" parameter to close disjointig gaps
* Various improvements and bugfixes

Flye 2.7.1. release (24 Apr 2020)
=================================
* Fixes very long GFA generation time for some large assemblies (no other changes)

Flye 2.7 release (03 Mar 2020)
==============================
* Better assemblies of real (and comlpex) metagenomes
* New option to retain alternative haplotypes, rather than collapsing them (`--keep-haplotypes`)
* PacBio HiFi mode
* Using Bam instead of Sam to reduce storage requirements and IO load
* Improved human assemblies
* Annotation of alternative contigs
* Better polishing quality for the newest ONT datasets
* Trestle module is disabled by default (use `--trestle` to enable)
* Many big fixes and improvements

Flye 2.6 release (19 Sep 2019)
==============================
* This release introduces Python 3 support (no other changes)

Flye 2.5 release (25 Jul 2019)
==============================
* Better ONT polishing for the latest basecallers (Guppy/flipflop)
* Improved consensus quality of repetitive regions
* More contiguous assemblies of real metagenomes
* Improvements for human genome assemblies
* Various bugfixes and performance optimizations

Flye 2.4.2 release (06 Apr 2019)
================================
* Improvements in k-mer selection and tip clipping for metagenome assemblies
* Better memory managment during consensus/polishing
* Some bugfixes

Flye 2.4.1 release (05 Mar 2019)
================================
* Speed and stability improvements for large datasets
* New option `--polish-target` to run Flye polisher on the target sequence


Flye 2.4 release (14 Jan 2019)
==============================
* Metagenome assembly support fully integrated (`--meta` option)
* New Trestle module for resolving simple unbridged repeats
* New `--plasmids` option that recovers short unassembled plasmids

Flye 2.3.7 (14 Nov 2018)
=======================
* Improvements in repeat edges detection
* More precise read mapping - more contiguous assemblies for some datasets
* Memory and performance optimizations for high-coverage datasets
* More accurate repeat graphs for complex datasets


Flye 2.3.6 (24 Sep 2018)
========================
* Memory consumption for large genome assemblies reduced by ~30%
* It could be reduced even further by using the new option --asm-coverage,
which specifies a subset of reads for initial contig assembly
* Better repeat graph representation for complex genomes
* Various bugfixes and stability improvements

Flye 2.3.5 (7 August 2018)
==========================
* New solid kmer alignment implementation with improved specificity
* Better corrected reads support
* Minimum overlap is now selected within a wider range for better support of datasets with shorter read length
* Assembly of large (human size) genomes is now faster
* Various bugfixes and stability improvements

Flye 2.3.4 (19 May 2018)
========================
* A fix for assemblies with low reads count
* Polishing of large genomes is now 2-3x faster and requires less memory

Flye 2.3.3 (27 Mar 2018)
========================
* Automatic selection of minimum overlap parameter based on read length
* Improvements in large genome assemblies
* Minimap2 updated
* Other bugfixes

Flye 2.3.2 (19 Feb 2018)
========================
* Better contiguity for larger genome assemblies
* Improvements in corrected reads mode
* Various bugfixes

Flye 2.3.1 (13 Jan 2018)
========================
* Minor release with a few bugs fixed

Flye 2.3 (04 Jan 2018)
======================

* ABruijn 2.x branch has been renamed to Flye, highlighting many substantial algorithmic changes
* Stable version of the repeat analysis module
* New command-line syntax (fallback mode with the old syntax is available)
* New --subassemblies mode for generating consensus of multiple assemblies
* Improved performance and reduced memory footprint (now scales to human genome)
* Corrected reads are now supported
* Extra output with information about the contigs (coverage, multiplicity, graph paths etc.)
* Gzipped Fasta/q support
* Multiple read files support
* Various bugfixes

ABruijn 2.2b (07 Oct 2017)
==========================

* Various bug fixes and improvements
* More accurate assembly graph construction
* Support for very long (100kb+) reads
* Fastq input

ABruijn 2.1b (11 Sep 2017)
==========================

* Various bug fixes and performance improvements

ABruijn 2.0b (25 Jul 2017)
==========================

* A new repeat graph analysis module for more complete and accurate assembly
* ABruijn now outputs a graph representation of the final assembly
* Significant improvements in performance and reduced memory footprint
* Various bugfixes
