EukRep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets (by patrickwest)
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EukRep Alternatives

Similar projects and alternatives to EukRep

  • metaGEM

    14 EukRep VS metaGEM

    :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

  • EukCC

    1 EukRep VS EukCC

    Tool to estimate genome quality of microbial eukaryotes

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  • merqury

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    k-mer based assembly evaluation

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    Genome assembly evaluation tool

  • CompareGenomeQualities

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    Reference free comparison of genome assemblies

  • SaaSHub

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NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a better EukRep alternative or higher similarity.
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EukRep reviews and mentions

Posts with mentions or reviews of EukRep. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-10-01.
  • Deciding on genome assembly software
    6 projects | /r/bioinformatics | 1 Oct 2021
    Have you looked into QUAST for comparison of assemblies? How big is the bacterial community? You may need to do some binning of your contigs to separate them into species specific genomes. I can suggest metaGEM (developed by me! should be online in NAR any day now) for generating MAGs for your bacterial species. Although it currently only supports short reads, it may give you an idea of what the bacterial community looks like. Maybe also look into EukCC for estimating fungal genome completeness and/or EukRep for splitting the contigs according to prokaryotic/eukaryotic provenance. You could also try estimating community composition directly from short read analysis using e.g. mOTUs2, kraken/braken, metaphlan, etc.

Stats

Basic EukRep repo stats
1
62
0.0
over 2 years ago

patrickwest/EukRep is an open source project licensed under MIT License which is an OSI approved license.

The primary programming language of EukRep is Python.

Popular Comparisons

  1. EukRep VS EukCC
  2. EukRep VS metaGEM
  3. EukRep VS quast
  4. EukRep VS merqury
  5. EukRep VS CompareGenomeQualities

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