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Flye 2.9
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@mikolmogorov mikolmogorov released this 21 Aug 18:27
· 84 commits to flye since this release
2.9
f6ec19e
  • 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
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