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Releases: mikolmogorov/Flye

Flye 2.9.5

27 Aug 15:54
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  • Python 3.12 support added, Python 2 dropped

Flye 2.9.4

24 May 14:24
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  • Minor technical changes

Flye 2.9.3

28 Nov 13:45
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  • Disjointig step speedup for --nano-hq mode
  • Improved --keep-haplotypes mode preserves more heterozygous SVs
  • A few bug fixes

Flye 2.9.2

18 Mar 15:51
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  • 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

07 Aug 16:44
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  • 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

21 Aug 18:27
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  • 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

10 Feb 21:58
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  • 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

09 Dec 17:20
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  • 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

02 Sep 23:18
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  • Added a new option --hifi-error to control the expected error rate of HiFi reads (no other changes)

Flye 2.8

05 Aug 01:27
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  • 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