RaGOO
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malonge
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
Fri Apr 2 10:42:44 2021 --- Running : /public/home/miniconda3/bin/minimap2 -k19 -w19 -t3 ..//public/home/ragoo/GCF_000298735.2_Oar_v4.0_genomic.fa ..//public/home/ragoo/hu.contig.fa > contigs_against_ref.paf 2> contigs_against_ref.paf.log Traceback (most recent call last): File "/public/home/soft/RaGOO-master/build/scripts-3.8/ragoo.py", line 585, in run(cmd) File...
When only running Assemblytics, there is a parameter to set the max_variant_size from 10kb to 10Mb, but RaGoo default max_variant_size 10kb, how to adjust it? Thanks~
Hi @malonge . I run ragtag and identified some sequences are unplaced. Is there anyway to find out which sequences were unplaced? I would like to do further analysis on...
Hi, when we used the corrected ONT Reads for the misassembly correction, there was some error in the *.misasm.break.fa file, when we use the command "less -S" open this file,...
Hi, I have produced ragoo.fasta file with using soapdenovo2 assembly as the input and a reference genome with its gff file. The command is below: `ragoo.py genome.fasta ref_genome.fna -m minimap2-master/minimap2...
Hi- thanks for the great tool! In the current version (v1.1), the output directory is hard-coded to be `ragoo_output`. Is there any plan to add a command line parameter to...
Hi, The `Contigs.txt` and `NbV1ChF.fasta` are 2.8 G and 2.6G. Minimap2 seems to run out of memory on 2TB machine. ``` $ ragoo.py -t 8 -g 100 -s -b -gff...
Hello, I see you have confidence scores associated with the grouping, localization, and orientation for each contig, and I want to know more details about it. For example, I have...
Dear Sir, I have run ragoo with -R parameter by executing as ragoo.py contigs.fasta reference.fasta -R short reads -T sr -C -g 111. It run well but it showed memory...
Hi, I'm setting un a pipeline to assemble short-read data at low coverage using a reference assembly of a very closely related species (GS: ~400Mb). Without going into details I...
