Comments (2)
Hi,
Currently Flye has very limited support for assembly of highly diploid genomes. Most likely in the assembly generated from raw reads some heterozugous alleles were collapsed. Is 15% an average value? 15% seems to be enough to not to be collapsed on the graph, but, say sequences that are divergent <10% already could be unintentionally glued (because we work with raw reads and expect high sequence divergence).
If you could send me the log file, I might have more thoughts on this. We are now also working on a new version that potentially may address this issue. In the mean time, starting with error-corrected reads seems to be a valid option as well (don't forget to use the corrected reads option).
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Closing this one - no activity since the last May.
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Related Issues (20)
- Option to display unassembled reads? HOT 1
- Is the final assembly function of the number of sequences ? HOT 6
- Is the name of the first contig in assembly.fasta always supposed to be contig_1? HOT 3
- Using fly to detect contamination in a pure culture? HOT 1
- Flye install fails with Python 3.12 HOT 2
- Command '['flye-modules', 'assemble', '--reads' HOT 2
- Better assembly with partial reads than full dataset HOT 2
- Positive and Negative Sense concatenating together for each contig HOT 16
- Flye output only 1 contig HOT 2
- Inclusion of reads <5000 results in increased fragmentation of assembly HOT 2
- How does Flye resolve 'unbridged' repeats? HOT 3
- No disjointigs were assembled(WARNING: No overlaps found - unable to estimate parameters)
- Best parameter for nanopore R9 HOT 6
- direct RNA Seq data with flye? HOT 1
- Metagenome HOT 1
- corrupted double-linked list HOT 3
- Meanings of both '--keep-halotypes' and '--no-alt-contigs'. HOT 7
- free(): invalid next size (fast) at "Simplifying the graph" HOT 4
- Assembly of complex genomes with high rate of genome rearrangements HOT 2
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