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## Version of Integron_Finder:
version 2
### OS
Linux
## Problem1: I/O overloaded for metagenomes with hundreds of thousands of contigs.
Usually, only a small subset of the contigs hav…
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Hello Daniel,
Just want to ask whether there are plans for also implement dartminhash (https://arxiv.org/abs/2005.11547), which is very fast for sparse dataset (genomes, metagenomes), and much fast…
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Hello,
I tried to redo a tree of life including my own metagenomes (~488) using the approach that you provide in examples (log file:
[phylophlan_tol.log](https://github.com/biobakery/phylophlan/fi…
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We're testing this implementation of the LazyB, MuCHSALSA, on a metagenome with both Illumina and Pacbio reads. We're testing these hybrid assemblies for soil metagenomes.
The first sample is still …
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I want to create a custom database using GTDB (genome taxonomy databse) where the protein sequences are identified by their accession number. I wrote a python script to find the Tax ID of each accessi…
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The accession BK010471 is for a crAssphage that is ubiquitous in human gut metagenomes ([link](https://www.nature.com/articles/ncomms5498)), and in particular is found in the 454 data set SRR073439.
…
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For very large metagenomes (~30 Gb size, 400 M reads) the spades reassembly can get bottlenecked during error/mismatch correction for hours. Removing the `--careful` flag from the spades call fixed th…
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I have a question that is likely a little outside of your scope for help. So, if there is another resource I should consult, could you please point me in that direction?
I used metawrap to bin ass…
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I've been working on doing gene-level summaries of metagenomes by exhaustively mapping reads with DIAMOND against a comprehensive non-redundant database of proteins (UniRef90). The result of this proc…
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@ctb I remember reading your blog about one use for sourmash and YAML would be to connect different researchers together.
I was wondering if such a database could help both to connect researchers and…