Flye

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Hi, We have nanopore reads sequenced with the Q20 but when I use nano-hq, there are no contigs assembled. However, when I use nano-raw, I get 4 contigs in the...

maguileraf

Cannot resolve link between two chromosomes- any other parameters I can adjust?

2

Hi, I have sequenced a haploid fungal genome (around 35mb total size, 7 chromosomes, 1 mitochondria) using both Nanopore (R10.4.1 Kit 14 ligation) and Illumina (150bp). I have removed middle...

zacksaud

Flye does not generate any output ("No disjointigs were assembled" message)

92

I have been trying to assemble a 10Mb genome with uncorrected nanopore data (3-4 chromosomes expected). We have a lot of data, is that the reason Flye fails at the...

StefanoLonardi

Flye assembly produces differentiating output on the same files.

11

Hi, Thanks for your great work on enabling de novo assembly on ONT data! I have been working on a snakemake pipeline for assembling and polishing bacterial data, and have...

KasperThystrup

metaFlye: PermissionError (Errno 1), no assembly_graph and assembly_info.txt. What to do?

1

Hi fenderglass and community, after running metaFlye with no interruptions I received the following Tracebacks and Errors (see below). The main output files should be assembly.fasta, assembly_graph.{gfa|gv} and assembly_info.txt. I...

Metag3nOmics

conda installer

18

Hello. I am using Ubuntu and I have tried python versions 3.5, 3.7, 3.9, and 2.7 and each time I get an error that my python version is wrong. I...

mr249

How to solve the problem about the high memory minimap2

6

Hello, author, thank you for developing the useful tools. I have successfully run it in another small genome of about 230MB, and got a very good assembly result.However, when I...

zhangwenda0518

no consensus with flye-minimap2

18

Hello, I am having problems with the consensus step of Flye 2.9-b1774 installed in anaconda3, where the pipeline aborts with: [2022-04-29 09:50:49] INFO: Starting Flye 2.9-b1774 [2022-04-29 09:50:50] INFO: >>>STAGE:...

twolfe

lh3/minimap2 please adopt your --secondary-seq patch

4

Hello, Debian Med wants to help where it can, hoping that bringing the Nanopore and associated software closer to a regular Linux distribution may attract additional eyeballs and help spread...

smoe

Incorrect haplotype polishing?

1

Hi, This issue is related to the `--polish-haplotypes` subcommand of the `--polish-target` command in the Flye version used by HapDup. Now, given a region, I have the following haplotypes from...

GuillaumeHolley