RaGOO
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malonge
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
Hi, It would be nice to have an optional parameter to choose the name of the output folder, which is always "ragoo_output". It seems it's not possible. Then we could...
Hello, I am trying to run get_contigs_border.py and get a KeyError for the first contig name in my orderings.txt file: ``` [rmaher@node03 ragoo_output]$ ../../../scripts/get_contig_borders.py orderings/orderings.txt ragoo.fasta.fai 100 Traceback (most recent...
Hello, As far as I understand, currently (v1.1) the only way to control the gap between contigs is by setting a uniform gap size through the padding parameter. It could...
This is a feature request - as of v1.1 the order of the contigs in each pseudomolecule is given in a separate TSV file. I think it would be more...
Hello, I ran RaGOO v1.1 with default parameters: `python ragoo.py contigs.fasta ref.fasta -t10` I looked for two specific contigs in the results which I know should map one after the...
It would be great to have RaGOO on Conda/Bioconda. Makes it easier to use it in SnakeMake and allows for analysis versioning. Thx!
Hi, I ran RaGOO, and 2,288,581,979 bp could be mapped to the reference, but 524,739,651 could not be aligned. How would it be possible to use the unmapped contigs and...
Hello, I am attempting to run Ragoo using a long-read assembly as the 'reference'. After running Ragoo with the following command: ``` ragoo.py -t 4 -b -C ${assembly} ${ref} ```...
Hi Michael! Thank you for the super-fast RaGOO algorithm! Do you have any good solutions for fast RaGOO out visualization? Do you have any idea how to visualize contigs_against_ref.paf and...
Hello, I have encountered the following errors when using this software. Can you help me solve them. /data/zhangkh/.conda/envs/ragoo/bin/ragoo.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('RaGOO==1.1', 'ragoo.py') Wed...
