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Hi,
I am currently trying to implement the metaGEM pipeline for the assembly and metabolic reconstruction of eukaryotic (particularly fungal) genomes. I was wondering if EukRep has been integrated …
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https://github.com/EBI-Metagenomics/genomes-pipeline/blob/853487f6dda1420fd8b6b41dd4aff5c8540c7e37/bin/fetch_ena.py#L66
The method above returns nothing. I believe it's because `metagenome_source` …
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In the run up to GSP we rapidly added many classes and fields to be able to accomodate all omics workflows and outputs. Post GSP we should return to this and fully document these, and map to existing …
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Hi,
I encouter below problem. How to deal with? Thank you very much!
2023-11-21 07:24:37 INFO: [MetadataReader 14212213139] Reading file: '/prj/hybrid-assembly/tmp/tmpfkd2zgz6/read_start_positions…
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Hello,
I am currently struggling with metagenomes obtained from environmental biofilms (river rocks). I have 50 metagenomes but I obtain only 100 checkV high-quality viruses. I would expect a lot m…
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Hi, not sure where to go with this so I'll start here to ask if anyone experienced something similar since I use tRNAscan-SE with bakta.
I noticed on tRNAscan-SE would run much slower the more thread…
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Redesign of the metagenome / sepsis report interface in the Vue app.
* add tabs for: read assignments, metagenome assembly, viral detection, genotypes and controls
* keep taxonomic read assignment…
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The phrasing *If you have less than 2 sequences, then ...* occurs at least three times for contig submission,
https://ena-docs.readthedocs.io/en/latest/submit/assembly/metagenome/mag.html#contig-as…
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[Breaking Lander-Waterman's Coverage Bound](http://biorxiv.org/content/early/2016/06/23/060384) - assembly
[Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads.](https://w…
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Trying to run CAMISIM to generate a very small test metagenome data set with a mixture of eukaryotic and prokaryotic genomes to test a pipeline with, following the example in the usage guide. I am get…