Ragout

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NetworkX 2.3 not supported

7

Dear support! Since NetworkX 2.3 requires Python 3.5+ (https://networkx.github.io/documentation/stable/install.html) && Ragout uses Python 2.7 it's impossible to run Ragout (or install via conda) with NetworkX 2.3 installed. I have to...

ipetrushin

Ragout error - TypeError: expected str, bytes or os.PathLike object, not NoneType

2

Since I read the paper for Ragout I've been really excited to use it for my work. I've been trying to improve a genome assembly for tree swallow using a...

ChuChuChaddy

"N"s in the output files

1

Hello, I was trying to use ragout in some files that are SPAdes outputs. It worked, but I noticed that the scaffolds file filled up some spaces with "N". What...

EllistonV

Required argument error with hal2mafMP.py

7

Hi Mikhail, I'm trying to get Ragout (2.3) running, however, it seems that HAL tools (2.1) are expecting a required argument that never gets passed to it. Specifically, at the...

bernard-kim

Alternative alignment tool

13

Good day, I'm currently working on the assembly of a large mammalian genome. I would like to perform the reference-assisted scaffolding using ragout. However, I cannot run progressive cactus on...

RenzoTale88

Hi, Do you have any recommendations for Phylogenetic tree tools which handle plant genomes? Thank you in advance. Michal

mictadlo

two small potential enhancements

2

Hello, I was wondering if ragout can implement the following two potential enhancements: 1) be able to sort the output contigs/scaffolds based on the chromosome/scaffold order (and maybe also orientation)...

yjx1217

ERROR: bad integers or strand in MAF (strand must be + for reference sequence) --

2

Hi, I ran multiple whole genome alignments using cactus to generate the hal file, and ran the "cactus-hal2maf js_hal2maf evolver27species.hal evolver27species.maf.gz --refGenome xxxx --chunkSize 500000" to transform the hal file....

chun-he-316

Six is not supported in Python3.12. Isn't it time to drop Python2 compatibility

1

Hi, in [file six.py](https://github.com/fenderglass/Ragout/blob/master/ragout/six.py#L21) you are implementing *"Utilities for writing code that runs on Python 2 and 3"*. Unfortunately this stops working for Python3.12. Debian (and probably other distributions) will...

tillea

How to check validity of results

1

Hi, i have ONT and Illumina PE data for a fungal genome with a size of 40Mbp. I have tried several methods to reach to a final assembly. My final...

Alexkortsi