Comments (3)
Yes, ideally it should be possible to learn the frequencies from the assembly, maybe in an iterative manner. Also, current nanopore profiles might be a bit outdated (generated with older chemistry) - we are planning to update them. Probably, the profile should also depend on a basecaller.
On the other hand, it seems that currently any kind of consensus from basecalled nanopore reads will not be perfect and require further polishing with raw signal / Illumina reads - so a quality improvement due a "corrected" error profile might not make a big difference.
from flye.
Also, I see that you guys are doing some work in the forked repository - this is exciting! Just a heads up - in the new version we are planning to change the repository structure / output format a bit (we are planning to release it in a week or two). I am trying to keep the commits as clean as possible to make the merging process easier (in case you will be interested).
from flye.
Thanks for the detailed answers. So having a look at the code and reading your response I guess the substitution matrix / homopolymer.mat is mainly used during polishing and bubble correction? In this case it would indeed not be very important to us since we anyway do a round of polishing using nanopolish and mapping Illumina reads as you say.
Second point; yes I forked your repo and integrated GraphMap (as discussed in an earlier thread, used a different account there so don't be confused :) ). I integrated it to a point where the automated installation, integration and running of GraphMap works perfectly on my side. But there is no documentation about the changes. I roughly tested it, but did not have time yet to check what difference it makes. For sure it takes much longer with GraphMap. So I'll do a pull request later and if you feel like testing GraphMap I'd be glad. But as you stated earlier, probably does not help much.
from flye.
Related Issues (20)
- 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
- Anomaly in resource usage HOT 7
- What parameter for R10.4.1 FAST mode data HOT 1
- Can't resume from a definite polishing step ? HOT 4
- flye usage HOT 1
- I am running an assembly on an ONT reads, but it was aborted HOT 1
- Flye assembler should support spaces in file paths. HOT 1
- Inferring number of elements in an assembly based on multiplicity HOT 2
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from flye.