-
Hello,
I am trying to mutate a rather large genome, here is the command:
python ~/bamsurgeon/bin/addsnv.py -v input_mutations.bed -f realvariants_Ayumu.sorted.golden.newheader.bam -r panTro6.auto…
-
Dear dRep team,
This is confusing to me when using mash sketch size 1000:
def run_mash_on_genome_chunks(genome_chunks, mash_exe, sketch_folder, MASH_folder, logdir, **kwargs):
dry = kwargs.…
-
Hi (not really an issue).
Could you be kind and add a little info/example on polishing the assembly? It was not clear from the ms how you did this.
It's probably just me (haven't assembled lar…
-
I've assembled a 1.3 Gb genome with hifiasm (version 0.14 e6e6dbf), merged both haplotypes and compared the kmer content to the read kmers with kat spectra-cn.
Because of a small heterozygocity of 0.…
-
hi everyone,
I'm successfully running Cactus through singularity container on a cluster. I've a few questions relating how to optimize parameters submitted to SLURM and possibly to Cactus itself:
…
-
This is related to #24 .
My hands are tied in the following sense, when polishing assembly of large genomes with deep coverage data:
1. I want to make use of the GPU acceleration
2. Using GPU l…
-
Hi!
Thank you for developing the tool! I'm working on a vertebrate genome (2.5Gb) and I was trying to run this as this looked the easiest. I'm aware that you have not tested on such large genomes b…
-
In the discussion with @Midnighter it came up that there should be a generic support for compressed files for the various io modules. I.e. cobrapy should support the reading and writing of compressed …
-
Hi,
I am working with a C. elegans laboratory which performs a large number of RNA-seq experiments. They love your tool, and we appreciate your work to make it user-friendly and to output quality f…
-
Hi James,
I'm trying to compare draft reconstructions of genome scale models for closely related strains of a species. Does sbml-diff have a functionality to only print the changes (maybe with a re…