Genome size parameter is no longer required (it is still needed for downsampling though -asm-coverage).
1.5-2x RAM footprint reduction for large assemblies (e.g.
This strategy is more robust to drops in coverage/contamination and requires less memory
Using the -meta k-mer selection strategy in isolate assemblies as well.
Improvements in contiguity and speed for PacBio HiFi mode.
Added a new option -hifi-error to control the expected error rate of HiFi reads (no other changes).
Speed improvements for graph simplification algorithms.
Improvements in GFA output, much faster generation of large and tangled graphs.
Assemblies should be largely identical to 2.8.
Fixed rare artificial sequence insertions on some ONT datasets.
Reduced RAM consumption for some ultra-long ONT datasets.
Several rare bug fixes/other improvements.
Contig paths output in Gfa + number of reads supporting each link (RC tag).
New -extra-params option to modify config-level parameters.
-trestle and -subassemblies modes are now deprecated, and will be removed in the future versions.
Discontinued -plasmid option due to the improvements in short sequences assembly.
Automatically selected minimum overlap up to 10k (was 5k).
Bam file input for the standalone polisher (same interface as for FASTA/Q).
Scaffolding is no longer performed by default (could be enabled with -scaffold).
Improvements in repeat detection algorithm to further limit a chance of (otherwise infrequent) misassemblies.
Polishing improvements: reduced number of possible clusters of errors.
Optimized default parameters for HiFi (HPC error threshold 0.01 -> 0.001 increased min overlap).
New -nano-hq mode for ONT Guppy5+ (SUP mode) and Q20 reads (3-5% error rate).
They were often missed in previous versions.
Better assembly of very short sequences (e.g.
To recover two phased haplotypesĬonsider applying HapDup after the assembly. Represented by a single mosaic haplotype. Pipeline: it takes raw PacBio / ONT reads as input and outputs polished contigs.įlye also has a special mode for metagenome assembly.Ĭurrently, Flye will produce collapsed assemblies of diploid genomes, It is designed for a wide range of datasets, from small bacterial projects Such as those produced by PacBio and Oxford Nanopore Technologies. Flye is a de novo assembler for single-molecule sequencing reads,