2.9.1 docs

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
+### Version: 2.9.1
 
 Flye is a de novo assembler for single-molecule sequencing reads,
 such as those produced by PacBio and Oxford Nanopore Technologies.
@@ -26,6 +26,13 @@ Manuals
 Latest updates
 --------------
 
+### 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 2021)
 * Better assembly of very short sequences (e.g. plasmids or viruses). They were often missed in previous versions.
 * New --nano-hq mode for ONT Guppy5+ (SUP mode) and Q20 reads (3-5% error rate)

docs/NEWS.md

@@ -1,3 +1,11 @@
+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.

docs/USAGE.md

@@ -64,6 +64,8 @@ optional arguments:
   --plasmids            unused (retained for backward compatibility)
   --meta                metagenome / uneven coverage mode
   --keep-haplotypes     do not collapse alternative haplotypes
+  --no-alt-contigs      do not output contigs representing alternative
+                        haplotypes
   --scaffold            enable scaffolding using graph [disabled by default]
   --trestle             [deprecated] enable Trestle [disabled by default]
   --polish-target path  run polisher on the target sequence
@@ -208,6 +210,12 @@ longer consensus contigs. The option `--keep-haplotypes` retains
 the alternative paths on the graph, producing less contigouos, but
 more detailed assembly.
 
+### Removing alternative contigs
+
+In default mode, Flye is performing collapsed/haploid assmebly,
+but may output contigs representing alternative alleles if they
+differ significatnly from the "primary" assmebled allele.
+To disable output of alternative contigs, use the `--no-alt-contigs` option.
 
 ### Scaffold
 
@@ -308,7 +316,8 @@ Scaffold gaps are marked with `??` symbols, and `*` symbol denotes a
 terminal graph node.
 
 Alternative contigs (representing alternative haplotypes) will have the same
-alt. group ID. Primary contigs are marked by `*`
+alt. group ID. Primary contigs are marked by `*`. Note that the ouptut of
+alternative contigs could be disabled via the `--no-alt-contigs` option.
 
 ## <a name="graph"></a> Repeat graph
 

flye/__build__.py

@@ -1 +1 @@
-__build__ = 1779
+__build__ = 1780

flye/__version__.py

@@ -1 +1 @@
-__version__ = "2.9"
+__version__ = "2.9.1"