From ec8ab677d4b47c472fc79300d1ec53f9f9b91ae2 Mon Sep 17 00:00:00 2001
From: Mikhail Kolmogorov <fenderglass@gmail.com>
Date: Tue, 28 Nov 2023 05:42:45 -0800
Subject: [PATCH] 2.9.3

---
 README.md           | 31 +++++++------------------------
 docs/NEWS.md        |  6 ++++++
 flye/__build__.py   |  2 +-
 flye/__version__.py |  2 +-
 4 files changed, 15 insertions(+), 26 deletions(-)

diff --git a/README.md b/README.md
index 0f8d2b776..5363ea5ac 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@ Flye assembler
 
 [![BioConda Install](https://img.shields.io/conda/dn/bioconda/flye.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/flye)
 
-### Version: 2.9.2
+### Version: 2.9.3
 
 Flye is a de novo assembler for single-molecule sequencing reads,
 such as those produced by PacBio and Oxford Nanopore Technologies.
@@ -26,6 +26,12 @@ Manuals
 Latest updates
 --------------
 
+### Flye 2.9.3 release (28 November 2023)
+* Disjointig step speedup for `--ont-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
@@ -54,29 +60,6 @@ Latest updates
 * 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 artificial sequence insertions on some ONT datasets
-* Assemblies 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 requires 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 disjointing gaps
-* Various improvements and bugfixes
-
 
 Repeat graph
 ------------
diff --git a/docs/NEWS.md b/docs/NEWS.md
index b5daab2e4..7f6d052c1 100644
--- a/docs/NEWS.md
+++ b/docs/NEWS.md
@@ -1,3 +1,9 @@
+Flye 2.9.3 release (28 November 2023)
+====================================
+* Disjointig step speedup for `--ont-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
diff --git a/flye/__build__.py b/flye/__build__.py
index b839c4f53..44e05f823 100644
--- a/flye/__build__.py
+++ b/flye/__build__.py
@@ -1 +1 @@
-__build__ = 1795
+__build__ = 1796
diff --git a/flye/__version__.py b/flye/__version__.py
index 4f1e6b1b5..a78f213cd 100644
--- a/flye/__version__.py
+++ b/flye/__version__.py
@@ -1 +1 @@
-__version__ = "2.9.2"
+__version__ = "2.9.3"