2.8.1

Author: mikolmogorov

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: 2.8
+### Version: 2.8.1
 
 Flye is a de novo assembler for single molecule sequencing reads,
 such as those produced by PacBio and Oxford Nanopore Technologies.
@@ -22,6 +22,9 @@ Manuals
 Latest updates
 --------------
 
+### 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.
@@ -128,7 +131,7 @@ The assemblies generated using Flye 2.8 could be downloaded from [Zenodo](https:
 All datasets were run with default parameters for the corresponding read type
 with the following exceptions: CHM13 T2T was run with `--min-overlap 10000 --asm-coverage 50`;
 CHM1 was run with `--asm-coverage 50`. CHM13 HiFi and HG002 HiFi datasets were run in
-`--pacbio-hifi` mode and reduced error rate threshold (0.003%).
+`--pacbio-hifi` mode and `--hifi-error 0.003`.
 
 Third-party
 -----------

docs/NEWS.md

@@ -1,3 +1,7 @@
+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

docs/USAGE.md

@@ -54,6 +54,8 @@ optional arguments:
                         minimum overlap between reads [auto]
   --asm-coverage int    reduced coverage for initial disjointig assembly [not
                         set]
+  --hifi-error float    expected HiFi reads error rate (e.g. 0.01 or 0.001)
+                        [0.01]
   --plasmids            rescue short unassembled plasmids
   --meta                metagenome / uneven coverage mode
   --keep-haplotypes     do not collapse alternative haplotypes
@@ -126,7 +128,9 @@ ONT data than with PacBio data, especially in homopolymer regions.
 ### PacBio HiFi
 
 Flye now supports assembly of PacBio HiFi protocol via `--pacbio-hifi` option.
-The expected read error is <1%.
+The expected read error is 1% by default. In case the reads are more accurate,
+you can adjust `--hifi-error` parameter (for example to 0.001) to potentially
+generate more complete assemblies.
 
 ### PacBio CLR
 
@@ -347,7 +351,7 @@ The assemblies generated using Flye 2.8 could be downloaded from [Zenodo](https:
 All datasets were run with default parameters for the corresponding read type
 with the following exceptions: CHM13 T2T was run with `--min-overlap 10000 --asm-coverage 50`;
 CHM1 was run with `--asm-coverage 50`. CHM13 HiFi and HG002 HiFi datasets were run in
-`--pacbio-hifi` mode and reduced error rate threshold (0.003%).
+`--pacbio-hifi` mode and `--hifi-error 0.003`.
 
 ## <a name="algorithm"></a> Algorithm Description
 

flye/__version__.py

@@ -1 +1 @@
-__version__ = "2.8"
+__version__ = "2.8.1"