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When using 30X hifi data, 0.16.1-r375 with default parameter produce a larger assembly fasta(the Genome size is estimated to be 2.2G, assembly result is 3.0G).Compared with the kmer distribution of an…
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in one of the closed issue says the Seg fault issue is fixed on v2.5 but I am still getting it on a 14gb genome:
pblat -threads=6 -noHead -fastMap -tileSize=12 -ooc=4461.ooc -minScore=100 -minIdentit…
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Hi,
ltr_finder, ltrharvest and LTR_retriever are quite slow in centier pipeline (expecially when the genome size is large), would please modify the code to accept existing scn file or LTR_retrieve…
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Hello, I am currently using the test.gfa file you provided to reproduce the results. However, when using the Dfam TE tools, I am unsure which dataset from the famdb library to use for comparison and c…
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I'm trying to build a custom db for GRiD (based on the UHGG database from https://www.ebi.ac.uk/metagenomics/genomes) and the update_database command died after running for several hours with the mess…
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I find it useful to see the absolute genomic coordinates when working with large chucks of DNA and even with genes, for instance, when working in parallel with other tools such as genome browsers or B…
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Hi,
I am attempting to perform a genome-guided assembly using Trinity. I have a BAM file aligned to the genome, and the command I used is:
singularity exec --bind /work /home/software/containers/tri…
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When I use concatenate.regions(GENOME.class), because the data is too large, the program uses the bigmemory package. Afterwards, when I execute GENOME.class
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I'm in the process of annotating the genome of _Icerya purchasi_ (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_952773005.1/) and have come across a large problem.
The final RepeatMasker annotat…
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Hello,
we have ~30x coverage ONT (N50 9.3 kb, 165 Gb) of a ~5 Gb plant genome and we would like to assemble it with Tulip - we wonder if it will run smoothly on such a genome.
To run it on a cluster…