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

Flye 2.7.1

• Fixes very long GFA generation time for some large assemblies (no other changes)