RagTag
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malonge
Tools for fast and flexible genome assembly scaffolding and improvement
Hello, I ran RagTag on plasmid contigs (correct; scaffold) and output files went to ragtag_output directory. this seems it worked (used one refernce sequence) fine (I received the nice Goodbye)....
Hi Malonge, I am new one for ragtag. when I run the command line with "ragtag.py patch ragtag_output/ragtag.scaffold.fasta ../reference.genome.fa -t 30 -u", I have some errors with following: Mon Aug...
# Hi # I am trying to install RagTag in Conda environment but getting the following error: (allenv) streptomyces@SBIO-KT-LIN-2:~/Rupesh/Kapil/kraken_processed_snippy$ conda install -c bioconda ragtag Collecting package metadata (current_repodata.json): done Solving...
Dear RagTag team, I was wondering if in any of the output files are stored the coordinates of the filled gaps in the in the input genome, the sequence used...
Dear RagTag team, Thanks for developing this useful tool! This post is a question and not an issue. I try to get an answer from other places like Biostar and...
Hello, I have a Pacbio CCS assembly (I used hifiasm as assembler). I also have a reference genome assembly (~2.8Gb) which contains several 500pb gaps. I used `ragtag patch` to...
Hi, First thanks for this great tool. I had get a scaffold sequence that some of its contain N bases, called `A.scaffold`. and I used contigs from nanopore using 'Necat'...
Hi @malonge Thank you for this tool. I would kindly want to ask if there was anyway to help prevent ragtag from leaving contig ids within the output scaffolded genome....
Hi, First thanks for this great tool. I see that there are a lot of people having trouble understanding how patch works, I read the wiki and the FAQ about...
Hi With the RagTag, I scaffolded a female plant assembly (as query) (HiFi assembled with IPA-contigs) using a male plant (Dovetail Omni-C scaffolded with HiFi-IPA). I used the default command/parameters:...
