diff --git a/README.md b/README.md index b8fe09828..739a5e2ca 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: 2.8 +### 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 ----------- diff --git a/docs/NEWS.md b/docs/NEWS.md index 65d991ecc..1561a4308 100644 --- a/docs/NEWS.md +++ b/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 diff --git a/docs/USAGE.md b/docs/USAGE.md index 754404477..1c3be801e 100644 --- a/docs/USAGE.md +++ b/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`. ## Algorithm Description diff --git a/flye/__version__.py b/flye/__version__.py index 2ac4c9174..b4066b65a 100644 --- a/flye/__version__.py +++ b/flye/__version__.py @@ -1 +1 @@ -__version__ = "2.8" +__version__ = "2.8.1"