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Thanks for a very interesting tool! I'm working with a very large (>20 Gb) draft genome assembly, so the default index size of 4 Gb for minimap2 requires 6 passes to complete alignments of reads to th…
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Hello,
I have two large genome files and would like to use SibeliaZ. I recently read this on a biostars thread "Yes, by SibeliaZ you can get .gfa file out of a fasta file. They recently updated the…
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Thank you for the best software for TE annotation. I use the RepeatModeler for one larger genome TE annotation, and find produce a few of files for rmblast alignment. I check the code ,and find the …
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## Is your feature request related to a problem? Please describe
Am working on in-planta infection RNAseq assays for the Lentil-Ascochyta pathosystem. The pathogen side of things works perfectl…
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Hi Developer
Look4ltrs runs for more than 10h without termination when run on
rice(NIP T2T https://www.cell.com/molecular-plant/pdfExtended/S1674-2052(23)00219-8)
maize(https://www.nature.com/a…
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### Description of feature
Currently testing TreeVal by running daSamNigr - the European elder.
The peptide subworkflow, is obviously slower however does not **require** any futher optimizations.
…
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I would like to use the pipeline on a large plant genome. Would it be to run separately on chromosomes or directly on the entire genome? Are there any requirements for CPUs and RAM? Have you ever test…
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I've been developing a metagenomic/metatranscriptomics software suite called VEBA (https://github.com/jolespin/veba) that natively handles eukaryotic binning of metagenome-assembled genomes and exon-a…
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Hi,
I am working on annotating large datasets, specifically Whole Genome Sequencing (WGS) VCF files, using the Variant Effect Predictor (VEP). However, the annotation process is taking significantl…
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Hello,
I am using modkit to study human methylation. However, the average size of a bed file containing three types of methylation is 300G, which is too large to be analyzed by my process, And i…