Michael Alonge

Hi there, RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag RagTag now uses pysam to query read coverage, so the memory requirement is dramatically reduced. Thanks, Mike

Hi there, Were you thinking something along the lines of a dotplot like mummerplot or assemblytics? Those both require base level alignments so the contigs_against_ref.paf can't be used for those....

Hi there, To answer your question more specifically, I wonder what relationship you want to study. It sounds like you want to use ragoo.fasta as a reference genome and use...

@mictadlo For SplitThreader, it looks like you need a VCF file and a CNV file. You can convert the assemblytics output format to VCF format [using SURVIVOR](https://github.com/malonge/RaGOO/wiki/Calling-Structural-Variants#output). I am not...

Hi there, This will be a feature in v2, which is what I am currently focusing on. Perhaps, after I release v2, I will revisit for v1 and add that...

Hi there, You can change the min and max SV size with `-a` and `-f` respectively. These are currently hidden parameters, but they will do the trick. By the way,...

Hi Lauren, Is the missing sequence present in unplaced contigs? They should be concatenated at the end of the `ragoo.fasta` since you used `-C`.

hmm so something definitely seems off. The first thing to check would be to ensure that every contig has been placed in an orderings files. Can you do `cat ragoo_output/orderings*.txt...

oh wow that is a ton of contigs! How many contigs are in your original assembly? And can you tell me what species you are assembling?

Well, in theory, it should work even for an assembly with so many contigs. As a test, perhaps you can run without `-C` and see if that works? I wonder...