Releases: mikolmogorov/Flye
Releases · mikolmogorov/Flye
Flye 2.9.5
- Python 3.12 support added, Python 2 dropped
Flye 2.9.4
- Minor technical changes
Flye 2.9.3
- Disjointig step speedup for
--nano-hq
mode - Improved
--keep-haplotypes
mode preserves more heterozygous SVs - A few bug fixes
Flye 2.9.2
- 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
- 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
- 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+ 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 detection 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
- 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
- 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
- Added a new option
--hifi-error
to control the expected error rate of HiFi reads (no other changes)
Flye 2.8
- 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 through
--asm-coverage
) - Flye now can occasionally use overlaps shorter than "minOverlap" parameter to close disjointig gaps
- Various improvements and bugfixes